Starting phenix.real_space_refine on Fri Mar 22 14:05:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/03_2024/5a1a_2984_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 160 5.16 5 Na 8 4.78 5 C 20816 2.51 5 N 5808 2.21 5 O 6896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B ARG 760": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 857": "NH1" <-> "NH2" Residue "B ARG 894": "NH1" <-> "NH2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 537": "OE1" <-> "OE2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 699": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C ARG 760": "NH1" <-> "NH2" Residue "C ARG 781": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "C ARG 857": "NH1" <-> "NH2" Residue "C ARG 894": "NH1" <-> "NH2" Residue "C ARG 917": "NH1" <-> "NH2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 446": "NH1" <-> "NH2" Residue "D ARG 473": "NH1" <-> "NH2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D GLU 537": "OE1" <-> "OE2" Residue "D ARG 561": "NH1" <-> "NH2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 699": "NH1" <-> "NH2" Residue "D ARG 721": "NH1" <-> "NH2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D ARG 760": "NH1" <-> "NH2" Residue "D ARG 781": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 857": "NH1" <-> "NH2" Residue "D ARG 894": "NH1" <-> "NH2" Residue "D ARG 917": "NH1" <-> "NH2" Residue "D GLU 943": "OE1" <-> "OE2" Residue "D ARG 952": "NH1" <-> "NH2" Residue "D ARG 961": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33696 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "B" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "C" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "D" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 9, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 950} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "D" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Time building chain proxies: 16.72, per 1000 atoms: 0.50 Number of scatterers: 33696 At special positions: 0 Unit cell: (191.737, 147.147, 102.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 Mg 8 11.99 Na 8 11.00 O 6896 8.00 N 5808 7.00 C 20816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.28 Conformation dependent library (CDL) restraints added in 5.9 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 52 sheets defined 12.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.744A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Proline residue: A 434 - end of helix removed outlier: 3.784A pdb=" N SER A 437 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 438 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR A 441 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG A 442 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.983A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.680A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 602 removed outlier: 3.742A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 617 through 623 Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 964 through 969 removed outlier: 3.624A pdb=" N MET A 968 " --> pdb=" O GLN A 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 969 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 969' Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 396 through 405 removed outlier: 3.744A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 Proline residue: B 434 - end of helix removed outlier: 3.784A pdb=" N SER B 437 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 438 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 441 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG B 442 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 445 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.983A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 549 through 558 removed outlier: 3.680A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 602 removed outlier: 3.742A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 599 through 602' Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 790 through 793 No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 964 through 969 removed outlier: 3.624A pdb=" N MET B 968 " --> pdb=" O GLN B 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 969 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 964 through 969' Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 396 through 405 removed outlier: 3.744A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 447 Proline residue: C 434 - end of helix removed outlier: 3.784A pdb=" N SER C 437 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 438 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR C 441 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG C 442 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 445 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.983A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 558 removed outlier: 3.680A pdb=" N TRP C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 602 removed outlier: 3.742A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 599 through 602' Processing helix chain 'C' and resid 617 through 623 Processing helix chain 'C' and resid 790 through 793 No H-bonds generated for 'chain 'C' and resid 790 through 793' Processing helix chain 'C' and resid 806 through 813 Processing helix chain 'C' and resid 964 through 969 removed outlier: 3.624A pdb=" N MET C 968 " --> pdb=" O GLN C 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 964 through 969' Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.744A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Proline residue: D 434 - end of helix removed outlier: 3.784A pdb=" N SER D 437 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 438 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR D 441 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG D 442 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 445 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 478 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.983A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 525' Processing helix chain 'D' and resid 549 through 558 removed outlier: 3.680A pdb=" N TRP D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 602 removed outlier: 3.742A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 599 through 602' Processing helix chain 'D' and resid 617 through 623 Processing helix chain 'D' and resid 790 through 793 No H-bonds generated for 'chain 'D' and resid 790 through 793' Processing helix chain 'D' and resid 806 through 813 Processing helix chain 'D' and resid 964 through 969 removed outlier: 3.624A pdb=" N MET D 968 " --> pdb=" O GLN D 964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 969 " --> pdb=" O GLN D 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 964 through 969' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= B, first strand: chain 'A' and resid 82 through 86 removed outlier: 8.504A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 160 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS A 154 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= E, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.659A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.037A pdb=" N ILE A 351 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 567 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY A 353 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 386 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG A 356 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG A 388 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR A 408 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS A 389 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 410 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP A 411 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP A 456 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 575 through 578 Processing sheet with id= I, first strand: chain 'A' and resid 627 through 629 Processing sheet with id= J, first strand: chain 'A' and resid 661 through 670 removed outlier: 6.696A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU A 650 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 694 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA A 723 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 696 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG A 721 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 698 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN A 719 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 700 " --> pdb=" O TRP A 717 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 717 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 739 through 742 removed outlier: 5.600A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 781 through 783 removed outlier: 6.553A pdb=" N LEU A 884 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 987 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS A 886 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN A 985 " --> pdb=" O CYS A 886 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 888 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP A 983 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 914 through 921 removed outlier: 3.792A pdb=" N THR A 867 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP A 842 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 851 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS A 840 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG A 853 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 838 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 855 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE A 836 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 857 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 834 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= O, first strand: chain 'B' and resid 82 through 86 removed outlier: 8.504A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 160 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 154 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP B 158 " --> pdb=" O CYS B 154 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 224 through 227 Processing sheet with id= R, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.659A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 335 through 338 Processing sheet with id= T, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.037A pdb=" N ILE B 351 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 567 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY B 353 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 386 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG B 356 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG B 388 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR B 408 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS B 389 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 410 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 411 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP B 456 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 575 through 578 Processing sheet with id= V, first strand: chain 'B' and resid 627 through 629 Processing sheet with id= W, first strand: chain 'B' and resid 661 through 670 removed outlier: 6.696A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU B 650 " --> pdb=" O PRO B 669 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 694 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA B 723 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 696 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG B 721 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 698 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN B 719 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 700 " --> pdb=" O TRP B 717 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP B 717 " --> pdb=" O VAL B 700 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 739 through 742 removed outlier: 5.600A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 781 through 783 removed outlier: 6.553A pdb=" N LEU B 884 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 987 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS B 886 " --> pdb=" O ASN B 985 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN B 985 " --> pdb=" O CYS B 886 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 888 " --> pdb=" O TRP B 983 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 983 " --> pdb=" O LEU B 888 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 914 through 921 removed outlier: 3.792A pdb=" N THR B 867 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 842 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE B 851 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS B 840 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG B 853 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 838 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 855 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE B 836 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 857 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 834 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= AB, first strand: chain 'C' and resid 82 through 86 removed outlier: 8.504A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 160 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 154 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 224 through 227 Processing sheet with id= AE, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.659A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 335 through 338 Processing sheet with id= AG, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.037A pdb=" N ILE C 351 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 567 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY C 353 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA C 386 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG C 356 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG C 388 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C 408 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS C 389 " --> pdb=" O TYR C 408 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 410 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP C 411 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP C 456 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 575 through 578 Processing sheet with id= AI, first strand: chain 'C' and resid 627 through 629 Processing sheet with id= AJ, first strand: chain 'C' and resid 661 through 670 removed outlier: 6.696A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU C 650 " --> pdb=" O PRO C 669 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 694 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA C 723 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 696 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG C 721 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 698 " --> pdb=" O GLN C 719 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN C 719 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 700 " --> pdb=" O TRP C 717 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP C 717 " --> pdb=" O VAL C 700 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 739 through 742 removed outlier: 5.600A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 781 through 783 removed outlier: 6.553A pdb=" N LEU C 884 " --> pdb=" O ASP C 987 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP C 987 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS C 886 " --> pdb=" O ASN C 985 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN C 985 " --> pdb=" O CYS C 886 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 888 " --> pdb=" O TRP C 983 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP C 983 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 914 through 921 removed outlier: 3.792A pdb=" N THR C 867 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP C 842 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE C 851 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS C 840 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG C 853 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR C 838 " --> pdb=" O ARG C 853 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 855 " --> pdb=" O ILE C 836 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE C 836 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 857 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 834 " --> pdb=" O ARG C 857 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= AO, first strand: chain 'D' and resid 82 through 86 removed outlier: 8.504A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 160 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS D 154 " --> pdb=" O TRP D 158 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.642A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= AR, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.659A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'D' and resid 335 through 338 Processing sheet with id= AT, first strand: chain 'D' and resid 564 through 567 removed outlier: 6.037A pdb=" N ILE D 351 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL D 567 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY D 353 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA D 386 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG D 356 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG D 388 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR D 408 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS D 389 " --> pdb=" O TYR D 408 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 410 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP D 411 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 456 " --> pdb=" O ASP D 411 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 575 through 578 Processing sheet with id= AV, first strand: chain 'D' and resid 627 through 629 Processing sheet with id= AW, first strand: chain 'D' and resid 661 through 670 removed outlier: 6.696A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU D 650 " --> pdb=" O PRO D 669 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 694 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA D 723 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU D 696 " --> pdb=" O ARG D 721 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG D 721 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL D 698 " --> pdb=" O GLN D 719 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN D 719 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL D 700 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP D 717 " --> pdb=" O VAL D 700 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'D' and resid 739 through 742 removed outlier: 5.600A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'D' and resid 781 through 783 removed outlier: 6.553A pdb=" N LEU D 884 " --> pdb=" O ASP D 987 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D 987 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS D 886 " --> pdb=" O ASN D 985 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN D 985 " --> pdb=" O CYS D 886 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 888 " --> pdb=" O TRP D 983 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP D 983 " --> pdb=" O LEU D 888 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'D' and resid 914 through 921 removed outlier: 3.792A pdb=" N THR D 867 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP D 842 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE D 851 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS D 840 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG D 853 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR D 838 " --> pdb=" O ARG D 853 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR D 855 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE D 836 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG D 857 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 834 " --> pdb=" O ARG D 857 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.46 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 12 1.09 - 1.27: 5516 1.27 - 1.45: 10120 1.45 - 1.63: 17972 1.63 - 1.81: 256 Bond restraints: 33876 Sorted by residual: bond pdb=" C GLU C 461 " pdb=" N SER C 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU B 461 " pdb=" N SER B 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU D 461 " pdb=" N SER D 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C GLU A 461 " pdb=" N SER A 462 " ideal model delta sigma weight residual 1.333 0.985 0.348 1.34e-02 5.57e+03 6.75e+02 bond pdb=" C VAL B 146 " pdb=" N ASN B 147 " ideal model delta sigma weight residual 1.331 0.912 0.419 1.66e-02 3.63e+03 6.36e+02 ... (remaining 33871 not shown) Histogram of bond angle deviations from ideal: 86.30 - 99.71: 8 99.71 - 113.13: 18984 113.13 - 126.54: 26356 126.54 - 139.96: 856 139.96 - 153.37: 12 Bond angle restraints: 46216 Sorted by residual: angle pdb=" O GLU C 461 " pdb=" C GLU C 461 " pdb=" N SER C 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU B 461 " pdb=" C GLU B 461 " pdb=" N SER B 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU A 461 " pdb=" C GLU A 461 " pdb=" N SER A 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O GLU D 461 " pdb=" C GLU D 461 " pdb=" N SER D 462 " ideal model delta sigma weight residual 122.59 153.37 -30.78 1.33e+00 5.65e-01 5.36e+02 angle pdb=" O ASN A 147 " pdb=" C ASN A 147 " pdb=" N SER A 148 " ideal model delta sigma weight residual 122.87 99.59 23.28 1.23e+00 6.61e-01 3.58e+02 ... (remaining 46211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 18360 17.63 - 35.27: 1176 35.27 - 52.90: 264 52.90 - 70.53: 60 70.53 - 88.17: 48 Dihedral angle restraints: 19908 sinusoidal: 8092 harmonic: 11816 Sorted by residual: dihedral pdb=" CA ILE D 882 " pdb=" C ILE D 882 " pdb=" N GLY D 883 " pdb=" CA GLY D 883 " ideal model delta harmonic sigma weight residual 180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ILE B 882 " pdb=" C ILE B 882 " pdb=" N GLY B 883 " pdb=" CA GLY B 883 " ideal model delta harmonic sigma weight residual -180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ILE C 882 " pdb=" C ILE C 882 " pdb=" N GLY C 883 " pdb=" CA GLY C 883 " ideal model delta harmonic sigma weight residual -180.00 -148.41 -31.59 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 19905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4224 0.056 - 0.112: 528 0.112 - 0.168: 72 0.168 - 0.225: 12 0.225 - 0.281: 4 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ASP A 507 " pdb=" N ASP A 507 " pdb=" C ASP A 507 " pdb=" CB ASP A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP C 507 " pdb=" N ASP C 507 " pdb=" C ASP C 507 " pdb=" CB ASP C 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP B 507 " pdb=" N ASP B 507 " pdb=" C ASP B 507 " pdb=" CB ASP B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4837 not shown) Planarity restraints: 6092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 460 " -0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN A 460 " 0.250 2.00e-02 2.50e+03 pdb=" O ASN A 460 " -0.096 2.00e-02 2.50e+03 pdb=" N GLU A 461 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 460 " 0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN D 460 " -0.250 2.00e-02 2.50e+03 pdb=" O ASN D 460 " 0.096 2.00e-02 2.50e+03 pdb=" N GLU D 461 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 460 " 0.076 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C ASN B 460 " -0.250 2.00e-02 2.50e+03 pdb=" O ASN B 460 " 0.096 2.00e-02 2.50e+03 pdb=" N GLU B 461 " 0.078 2.00e-02 2.50e+03 ... (remaining 6089 not shown) Histogram of nonbonded interaction distances: 0.02 - 1.00: 10 1.00 - 1.97: 0 1.97 - 2.95: 15618 2.95 - 3.92: 99552 3.92 - 4.90: 195510 Warning: very small nonbonded interaction distances. Nonbonded interactions: 310690 Sorted by model distance: nonbonded pdb=" O HOH B5087 " pdb=" O HOH C5084 " model vdw 0.020 2.440 nonbonded pdb=" O HOH A5087 " pdb=" O HOH D5084 " model vdw 0.020 2.440 nonbonded pdb=" O HOH B5084 " pdb=" O HOH C5087 " model vdw 0.020 2.440 nonbonded pdb=" O HOH A5084 " pdb=" O HOH D5087 " model vdw 0.020 2.440 nonbonded pdb=" O HOH B5085 " pdb=" O HOH C5085 " model vdw 0.021 2.440 ... (remaining 310685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.190 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 89.540 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.419 33876 Z= 0.565 Angle : 1.213 30.785 46216 Z= 0.843 Chirality : 0.039 0.281 4840 Planarity : 0.005 0.145 6092 Dihedral : 13.177 88.168 12300 Min Nonbonded Distance : 0.020 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.92 % Favored : 95.49 % Rotamer: Outliers : 1.03 % Allowed : 7.89 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 4080 helix: -2.30 (0.18), residues: 536 sheet: -0.14 (0.15), residues: 1120 loop : -1.56 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 90 HIS 0.002 0.001 HIS B 713 PHE 0.006 0.001 PHE B 512 TYR 0.008 0.001 TYR C 856 ARG 0.002 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 788 time to evaluate : 4.087 Fit side-chains REVERT: A 84 VAL cc_start: 0.6775 (m) cc_final: 0.6542 (m) REVERT: A 233 ASP cc_start: 0.5656 (m-30) cc_final: 0.5381 (m-30) REVERT: A 277 GLU cc_start: 0.5751 (pm20) cc_final: 0.5476 (tt0) REVERT: A 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: A 677 LYS cc_start: 0.7208 (ptmt) cc_final: 0.6918 (ptpp) REVERT: A 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6285 (mp10) REVERT: A 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5903 (mm-30) REVERT: B 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: B 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5383 (m-30) REVERT: B 277 GLU cc_start: 0.5749 (pm20) cc_final: 0.5473 (tt0) REVERT: B 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: B 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6919 (ptpp) REVERT: B 817 GLN cc_start: 0.6512 (mt0) cc_final: 0.6286 (mp10) REVERT: B 893 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5904 (mm-30) REVERT: C 84 VAL cc_start: 0.6777 (m) cc_final: 0.6544 (m) REVERT: C 233 ASP cc_start: 0.5659 (m-30) cc_final: 0.5384 (m-30) REVERT: C 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: C 537 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: C 677 LYS cc_start: 0.7209 (ptmt) cc_final: 0.6918 (ptpp) REVERT: C 817 GLN cc_start: 0.6511 (mt0) cc_final: 0.6286 (mp10) REVERT: C 893 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5903 (mm-30) REVERT: D 84 VAL cc_start: 0.6777 (m) cc_final: 0.6545 (m) REVERT: D 233 ASP cc_start: 0.5658 (m-30) cc_final: 0.5383 (m-30) REVERT: D 277 GLU cc_start: 0.5750 (pm20) cc_final: 0.5475 (tt0) REVERT: D 537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: D 677 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6917 (ptpp) REVERT: D 817 GLN cc_start: 0.6513 (mt0) cc_final: 0.6286 (mp10) REVERT: D 893 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5905 (mm-30) outliers start: 36 outliers final: 4 residues processed: 812 average time/residue: 1.5611 time to fit residues: 1495.2696 Evaluate side-chains 508 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 500 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 0.0870 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 30 HIS A 38 ASN A 89 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 355 ASN A 391 HIS A 395 HIS A 485 GLN A 573 GLN A 597 ASN A 653 HIS A 757 GLN A 767 GLN A 775 GLN A 783 GLN ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 863 GLN A 896 ASN A 935 ASN A 985 ASN A1015 HIS B 25 ASN B 30 HIS B 38 ASN B 89 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 355 ASN B 391 HIS B 395 HIS B 485 GLN B 573 GLN B 597 ASN B 653 HIS B 757 GLN B 767 GLN B 775 GLN B 783 GLN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 863 GLN B 896 ASN B 935 ASN B 985 ASN C 25 ASN C 30 HIS C 38 ASN C 89 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 355 ASN C 391 HIS C 395 HIS C 485 GLN C 573 GLN C 597 ASN C 653 HIS C 757 GLN C 767 GLN C 775 GLN C 783 GLN ** C 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 863 GLN C 896 ASN C 935 ASN C 985 ASN C1015 HIS D 25 ASN D 30 HIS D 38 ASN D 89 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 355 ASN D 391 HIS D 395 HIS D 485 GLN D 573 GLN D 597 ASN D 653 HIS D 757 GLN D 767 GLN D 775 GLN D 783 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 863 GLN D 896 ASN D 935 ASN D 985 ASN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33876 Z= 0.205 Angle : 0.631 9.631 46216 Z= 0.327 Chirality : 0.044 0.153 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.839 87.607 4604 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 3.55 % Allowed : 13.16 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4080 helix: -1.14 (0.21), residues: 560 sheet: 0.06 (0.13), residues: 1384 loop : -0.86 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 90 HIS 0.007 0.001 HIS C 395 PHE 0.011 0.002 PHE D 63 TYR 0.012 0.002 TYR C 100 ARG 0.005 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 528 time to evaluate : 3.799 Fit side-chains REVERT: A 84 VAL cc_start: 0.7201 (m) cc_final: 0.6943 (m) REVERT: A 144 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6634 (t70) REVERT: A 233 ASP cc_start: 0.5590 (m-30) cc_final: 0.5337 (m-30) REVERT: A 277 GLU cc_start: 0.5983 (pm20) cc_final: 0.5714 (tt0) REVERT: A 326 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6613 (mm-30) REVERT: A 677 LYS cc_start: 0.7268 (ptmt) cc_final: 0.6954 (ptpp) REVERT: A 745 MET cc_start: 0.3234 (tpt) cc_final: 0.3005 (tpp) REVERT: A 782 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: B 84 VAL cc_start: 0.7201 (m) cc_final: 0.6943 (m) REVERT: B 144 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6632 (t70) REVERT: B 233 ASP cc_start: 0.5588 (m-30) cc_final: 0.5336 (m-30) REVERT: B 277 GLU cc_start: 0.5984 (pm20) cc_final: 0.5715 (tt0) REVERT: B 326 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: B 677 LYS cc_start: 0.7267 (ptmt) cc_final: 0.6955 (ptpp) REVERT: B 745 MET cc_start: 0.3235 (tpt) cc_final: 0.3003 (tpp) REVERT: B 782 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: C 84 VAL cc_start: 0.7201 (m) cc_final: 0.6945 (m) REVERT: C 144 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6631 (t70) REVERT: C 233 ASP cc_start: 0.5590 (m-30) cc_final: 0.5338 (m-30) REVERT: C 277 GLU cc_start: 0.5983 (pm20) cc_final: 0.5714 (tt0) REVERT: C 326 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: C 677 LYS cc_start: 0.7270 (ptmt) cc_final: 0.6957 (ptpp) REVERT: C 745 MET cc_start: 0.3235 (tpt) cc_final: 0.3003 (tpp) REVERT: C 782 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: D 84 VAL cc_start: 0.7202 (m) cc_final: 0.6945 (m) REVERT: D 144 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6634 (t70) REVERT: D 233 ASP cc_start: 0.5589 (m-30) cc_final: 0.5336 (m-30) REVERT: D 277 GLU cc_start: 0.5982 (pm20) cc_final: 0.5714 (tt0) REVERT: D 326 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: D 677 LYS cc_start: 0.7269 (ptmt) cc_final: 0.6955 (ptpp) REVERT: D 745 MET cc_start: 0.3234 (tpt) cc_final: 0.3004 (tpp) REVERT: D 782 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7315 (m-30) outliers start: 124 outliers final: 48 residues processed: 608 average time/residue: 1.5770 time to fit residues: 1131.5728 Evaluate side-chains 524 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 464 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 266 GLN A 395 HIS A 485 GLN A 573 GLN A 583 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 791 ASN A 985 ASN B 30 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 266 GLN B 395 HIS B 485 GLN B 573 GLN B 583 ASN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN B 791 ASN B 985 ASN B1015 HIS C 30 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 266 GLN C 395 HIS C 485 GLN C 573 GLN C 583 ASN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 GLN C 791 ASN C 985 ASN D 30 HIS ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 266 GLN D 395 HIS D 485 GLN D 573 GLN D 583 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 783 GLN D 791 ASN D 985 ASN D1015 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33876 Z= 0.343 Angle : 0.754 10.146 46216 Z= 0.390 Chirality : 0.049 0.157 4840 Planarity : 0.006 0.061 6092 Dihedral : 5.604 68.361 4580 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 5.15 % Allowed : 14.30 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4080 helix: -1.06 (0.22), residues: 548 sheet: 0.10 (0.13), residues: 1388 loop : -0.76 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 553 HIS 0.007 0.002 HIS C 30 PHE 0.018 0.003 PHE D 63 TYR 0.020 0.003 TYR D 123 ARG 0.006 0.001 ARG C 561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 504 time to evaluate : 3.901 Fit side-chains REVERT: A 52 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6876 (ttm-80) REVERT: A 144 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6700 (t70) REVERT: A 233 ASP cc_start: 0.5665 (m-30) cc_final: 0.5453 (m-30) REVERT: A 255 ARG cc_start: 0.7522 (mmt-90) cc_final: 0.7075 (mpt180) REVERT: A 277 GLU cc_start: 0.6175 (pm20) cc_final: 0.5889 (tt0) REVERT: A 326 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: A 611 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.4115 (ptp-170) REVERT: A 677 LYS cc_start: 0.7466 (ptmt) cc_final: 0.7109 (ptpp) REVERT: A 745 MET cc_start: 0.3394 (tpt) cc_final: 0.3059 (tpp) REVERT: A 782 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: A 934 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: A 965 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: B 52 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6877 (ttm-80) REVERT: B 144 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6701 (t70) REVERT: B 233 ASP cc_start: 0.5663 (m-30) cc_final: 0.5451 (m-30) REVERT: B 255 ARG cc_start: 0.7522 (mmt-90) cc_final: 0.7075 (mpt180) REVERT: B 277 GLU cc_start: 0.6175 (pm20) cc_final: 0.5890 (tt0) REVERT: B 326 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: B 611 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.4115 (ptp-170) REVERT: B 677 LYS cc_start: 0.7464 (ptmt) cc_final: 0.7106 (ptpp) REVERT: B 745 MET cc_start: 0.3392 (tpt) cc_final: 0.3058 (tpp) REVERT: B 782 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: B 934 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: B 965 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: C 52 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6878 (ttm-80) REVERT: C 144 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6700 (t70) REVERT: C 233 ASP cc_start: 0.5665 (m-30) cc_final: 0.5452 (m-30) REVERT: C 255 ARG cc_start: 0.7522 (mmt-90) cc_final: 0.7073 (mpt180) REVERT: C 277 GLU cc_start: 0.6175 (pm20) cc_final: 0.5890 (tt0) REVERT: C 326 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: C 611 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.4116 (ptp-170) REVERT: C 677 LYS cc_start: 0.7466 (ptmt) cc_final: 0.7109 (ptpp) REVERT: C 745 MET cc_start: 0.3394 (tpt) cc_final: 0.3059 (tpp) REVERT: C 782 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: C 934 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6662 (tp30) REVERT: C 965 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 52 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6876 (ttm-80) REVERT: D 144 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6701 (t70) REVERT: D 233 ASP cc_start: 0.5664 (m-30) cc_final: 0.5451 (m-30) REVERT: D 255 ARG cc_start: 0.7522 (mmt-90) cc_final: 0.7075 (mpt180) REVERT: D 277 GLU cc_start: 0.6176 (pm20) cc_final: 0.5891 (tt0) REVERT: D 326 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: D 611 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.4114 (ptp-170) REVERT: D 677 LYS cc_start: 0.7464 (ptmt) cc_final: 0.7108 (ptpp) REVERT: D 745 MET cc_start: 0.3392 (tpt) cc_final: 0.3057 (tpp) REVERT: D 782 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: D 934 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: D 965 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7455 (tm-30) outliers start: 180 outliers final: 84 residues processed: 632 average time/residue: 1.5384 time to fit residues: 1153.7719 Evaluate side-chains 556 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 444 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 266 GLN A 485 GLN A 554 GLN A 573 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 394 ASN B 485 GLN B 554 GLN B 573 GLN ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 485 GLN C 554 GLN C 573 GLN ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 485 GLN D 554 GLN D 573 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33876 Z= 0.233 Angle : 0.655 10.026 46216 Z= 0.334 Chirality : 0.045 0.160 4840 Planarity : 0.005 0.040 6092 Dihedral : 5.354 70.190 4580 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 4.72 % Allowed : 15.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4080 helix: -0.87 (0.22), residues: 548 sheet: 0.22 (0.14), residues: 1360 loop : -0.76 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 553 HIS 0.008 0.001 HIS A 30 PHE 0.012 0.002 PHE D 63 TYR 0.016 0.002 TYR B 100 ARG 0.006 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 455 time to evaluate : 3.749 Fit side-chains REVERT: A 144 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6687 (t70) REVERT: A 233 ASP cc_start: 0.5679 (m-30) cc_final: 0.5465 (m-30) REVERT: A 255 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.7260 (mmt-90) REVERT: A 277 GLU cc_start: 0.6174 (pm20) cc_final: 0.5871 (tt0) REVERT: A 292 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6795 (mtt180) REVERT: A 326 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 611 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.4174 (ptp-170) REVERT: A 677 LYS cc_start: 0.7361 (ptmt) cc_final: 0.6949 (ptpp) REVERT: A 745 MET cc_start: 0.3431 (tpt) cc_final: 0.3086 (tpp) REVERT: A 782 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: A 824 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.6050 (tt0) REVERT: A 965 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 144 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6688 (t70) REVERT: B 233 ASP cc_start: 0.5677 (m-30) cc_final: 0.5462 (m-30) REVERT: B 255 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.7259 (mmt-90) REVERT: B 277 GLU cc_start: 0.6174 (pm20) cc_final: 0.5870 (tt0) REVERT: B 292 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6797 (mtt180) REVERT: B 326 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: B 611 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.4173 (ptp-170) REVERT: B 677 LYS cc_start: 0.7361 (ptmt) cc_final: 0.6948 (ptpp) REVERT: B 745 MET cc_start: 0.3431 (tpt) cc_final: 0.3087 (tpp) REVERT: B 782 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: B 824 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: B 965 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: C 144 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6689 (t70) REVERT: C 233 ASP cc_start: 0.5678 (m-30) cc_final: 0.5465 (m-30) REVERT: C 255 ARG cc_start: 0.7507 (mmt-90) cc_final: 0.7259 (mmt-90) REVERT: C 277 GLU cc_start: 0.6173 (pm20) cc_final: 0.5870 (tt0) REVERT: C 292 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6796 (mtt180) REVERT: C 326 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: C 611 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.4173 (ptp-170) REVERT: C 677 LYS cc_start: 0.7363 (ptmt) cc_final: 0.6950 (ptpp) REVERT: C 745 MET cc_start: 0.3433 (tpt) cc_final: 0.3088 (tpp) REVERT: C 782 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: C 824 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.6050 (tt0) REVERT: C 965 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 144 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6686 (t70) REVERT: D 233 ASP cc_start: 0.5678 (m-30) cc_final: 0.5464 (m-30) REVERT: D 255 ARG cc_start: 0.7507 (mmt-90) cc_final: 0.7259 (mmt-90) REVERT: D 277 GLU cc_start: 0.6173 (pm20) cc_final: 0.5870 (tt0) REVERT: D 292 ARG cc_start: 0.7068 (mtt90) cc_final: 0.6795 (mtt180) REVERT: D 326 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: D 611 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.4172 (ptp-170) REVERT: D 677 LYS cc_start: 0.7361 (ptmt) cc_final: 0.6947 (ptpp) REVERT: D 745 MET cc_start: 0.3430 (tpt) cc_final: 0.3086 (tpp) REVERT: D 782 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: D 824 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: D 965 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7481 (tm-30) outliers start: 165 outliers final: 100 residues processed: 588 average time/residue: 1.5859 time to fit residues: 1099.4318 Evaluate side-chains 556 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 432 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 924 ASP Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 968 MET Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 MET Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 924 ASP Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 336 optimal weight: 0.0050 chunk 272 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 5.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 266 GLN A 395 HIS A 485 GLN A 510 GLN A 573 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 395 HIS B 485 GLN B 510 GLN B 573 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 395 HIS C 485 GLN C 510 GLN C 573 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 395 HIS D 485 GLN D 510 GLN D 573 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33876 Z= 0.239 Angle : 0.651 9.921 46216 Z= 0.332 Chirality : 0.045 0.148 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.352 71.015 4580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 5.43 % Allowed : 15.50 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4080 helix: -0.76 (0.22), residues: 548 sheet: 0.20 (0.14), residues: 1352 loop : -0.74 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 553 HIS 0.008 0.001 HIS B 30 PHE 0.012 0.002 PHE C 63 TYR 0.016 0.002 TYR A1014 ARG 0.006 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 448 time to evaluate : 4.210 Fit side-chains REVERT: A 52 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6864 (ttm-80) REVERT: A 144 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6690 (t70) REVERT: A 233 ASP cc_start: 0.5842 (m-30) cc_final: 0.5630 (m-30) REVERT: A 255 ARG cc_start: 0.7350 (mmt-90) cc_final: 0.7139 (mmt-90) REVERT: A 277 GLU cc_start: 0.6189 (pm20) cc_final: 0.5918 (tt0) REVERT: A 546 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 611 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.4049 (ptp-170) REVERT: A 677 LYS cc_start: 0.7168 (ptmt) cc_final: 0.6851 (ptpp) REVERT: A 745 MET cc_start: 0.3385 (tpt) cc_final: 0.2997 (tpp) REVERT: A 782 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: A 934 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: A 965 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: B 52 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6864 (ttm-80) REVERT: B 144 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6689 (t70) REVERT: B 233 ASP cc_start: 0.5842 (m-30) cc_final: 0.5629 (m-30) REVERT: B 255 ARG cc_start: 0.7352 (mmt-90) cc_final: 0.7141 (mmt-90) REVERT: B 277 GLU cc_start: 0.6189 (pm20) cc_final: 0.5919 (tt0) REVERT: B 546 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7283 (mp) REVERT: B 611 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.4090 (ptp-170) REVERT: B 677 LYS cc_start: 0.7168 (ptmt) cc_final: 0.6850 (ptpp) REVERT: B 745 MET cc_start: 0.3388 (tpt) cc_final: 0.3007 (tpp) REVERT: B 782 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: B 965 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: C 52 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6865 (ttm-80) REVERT: C 144 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6690 (t70) REVERT: C 233 ASP cc_start: 0.5842 (m-30) cc_final: 0.5631 (m-30) REVERT: C 255 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7140 (mmt-90) REVERT: C 277 GLU cc_start: 0.6190 (pm20) cc_final: 0.5919 (tt0) REVERT: C 546 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7286 (mp) REVERT: C 611 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.4091 (ptp-170) REVERT: C 677 LYS cc_start: 0.7168 (ptmt) cc_final: 0.6851 (ptpp) REVERT: C 745 MET cc_start: 0.3386 (tpt) cc_final: 0.2999 (tpp) REVERT: C 782 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: C 934 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: C 965 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: D 52 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6865 (ttm-80) REVERT: D 144 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6690 (t70) REVERT: D 233 ASP cc_start: 0.5842 (m-30) cc_final: 0.5629 (m-30) REVERT: D 255 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7141 (mmt-90) REVERT: D 277 GLU cc_start: 0.6190 (pm20) cc_final: 0.5918 (tt0) REVERT: D 546 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7289 (mp) REVERT: D 611 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.4092 (ptp-170) REVERT: D 677 LYS cc_start: 0.7167 (ptmt) cc_final: 0.6850 (ptpp) REVERT: D 745 MET cc_start: 0.3387 (tpt) cc_final: 0.3000 (tpp) REVERT: D 782 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: D 934 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: D 965 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7499 (tm-30) outliers start: 190 outliers final: 97 residues processed: 592 average time/residue: 1.5870 time to fit residues: 1115.7381 Evaluate side-chains 549 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 424 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 40.0000 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 266 GLN A 485 GLN A 573 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 485 GLN B 573 GLN B 761 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 485 GLN C 573 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 485 GLN D 573 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33876 Z= 0.233 Angle : 0.645 9.913 46216 Z= 0.328 Chirality : 0.045 0.158 4840 Planarity : 0.005 0.040 6092 Dihedral : 5.340 71.002 4580 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 4.75 % Allowed : 16.88 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4080 helix: -0.69 (0.22), residues: 548 sheet: 0.22 (0.14), residues: 1352 loop : -0.78 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 553 HIS 0.007 0.001 HIS C 30 PHE 0.012 0.002 PHE B 63 TYR 0.016 0.002 TYR C 100 ARG 0.005 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 455 time to evaluate : 4.279 Fit side-chains REVERT: A 41 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6638 (tt0) REVERT: A 52 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7042 (ttm-80) REVERT: A 233 ASP cc_start: 0.5889 (m-30) cc_final: 0.5681 (m-30) REVERT: A 277 GLU cc_start: 0.6170 (pm20) cc_final: 0.5891 (tt0) REVERT: A 546 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7233 (mp) REVERT: A 611 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.4128 (ptp-170) REVERT: A 677 LYS cc_start: 0.7157 (ptmt) cc_final: 0.6841 (ptpp) REVERT: A 745 MET cc_start: 0.3293 (tpt) cc_final: 0.2974 (tpp) REVERT: A 782 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: A 934 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: A 965 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 41 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6634 (tt0) REVERT: B 52 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7042 (ttm-80) REVERT: B 233 ASP cc_start: 0.5887 (m-30) cc_final: 0.5679 (m-30) REVERT: B 277 GLU cc_start: 0.6168 (pm20) cc_final: 0.5889 (tt0) REVERT: B 546 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 611 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.3850 (ptp-170) REVERT: B 677 LYS cc_start: 0.7156 (ptmt) cc_final: 0.6838 (ptpp) REVERT: B 745 MET cc_start: 0.3263 (tpt) cc_final: 0.2953 (tpp) REVERT: B 782 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: B 934 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: B 965 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: C 41 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6636 (tt0) REVERT: C 52 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7043 (ttm-80) REVERT: C 233 ASP cc_start: 0.5890 (m-30) cc_final: 0.5681 (m-30) REVERT: C 277 GLU cc_start: 0.6169 (pm20) cc_final: 0.5890 (tt0) REVERT: C 546 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7232 (mp) REVERT: C 611 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.3823 (ptp-170) REVERT: C 677 LYS cc_start: 0.7158 (ptmt) cc_final: 0.6841 (ptpp) REVERT: C 745 MET cc_start: 0.3294 (tpt) cc_final: 0.2976 (tpp) REVERT: C 782 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: C 934 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: C 965 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: D 41 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6636 (tt0) REVERT: D 52 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7041 (ttm-80) REVERT: D 233 ASP cc_start: 0.5891 (m-30) cc_final: 0.5680 (m-30) REVERT: D 277 GLU cc_start: 0.6170 (pm20) cc_final: 0.5891 (tt0) REVERT: D 546 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7236 (mp) REVERT: D 611 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.4127 (ptp-170) REVERT: D 677 LYS cc_start: 0.7157 (ptmt) cc_final: 0.6839 (ptpp) REVERT: D 745 MET cc_start: 0.3295 (tpt) cc_final: 0.2977 (tpp) REVERT: D 782 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: D 934 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: D 965 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7503 (tm-30) outliers start: 166 outliers final: 105 residues processed: 591 average time/residue: 1.5225 time to fit residues: 1071.0014 Evaluate side-chains 557 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 428 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 266 GLN A 395 HIS A 485 GLN A 573 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 395 HIS B 485 GLN B 573 GLN B 761 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 395 HIS C 485 GLN C 573 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 395 HIS D 485 GLN D 573 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33876 Z= 0.253 Angle : 0.668 9.930 46216 Z= 0.340 Chirality : 0.046 0.150 4840 Planarity : 0.005 0.043 6092 Dihedral : 5.437 72.075 4580 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 5.15 % Allowed : 16.70 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4080 helix: -0.74 (0.22), residues: 552 sheet: 0.27 (0.14), residues: 1304 loop : -0.84 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 553 HIS 0.010 0.001 HIS A 30 PHE 0.012 0.002 PHE A 33 TYR 0.017 0.002 TYR C 100 ARG 0.004 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 452 time to evaluate : 3.872 Fit side-chains REVERT: A 233 ASP cc_start: 0.5928 (m-30) cc_final: 0.5720 (m-30) REVERT: A 277 GLU cc_start: 0.6191 (pm20) cc_final: 0.5898 (tt0) REVERT: A 546 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7249 (mp) REVERT: A 610 ASP cc_start: 0.6196 (p0) cc_final: 0.5925 (p0) REVERT: A 611 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.4047 (ptp-170) REVERT: A 745 MET cc_start: 0.3337 (tpt) cc_final: 0.3013 (tpp) REVERT: A 782 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: A 934 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: A 965 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 233 ASP cc_start: 0.5927 (m-30) cc_final: 0.5719 (m-30) REVERT: B 277 GLU cc_start: 0.6190 (pm20) cc_final: 0.5897 (tt0) REVERT: B 546 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7248 (mp) REVERT: B 610 ASP cc_start: 0.6196 (p0) cc_final: 0.5927 (p0) REVERT: B 611 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.4047 (ptp-170) REVERT: B 745 MET cc_start: 0.3320 (tpt) cc_final: 0.3001 (tpp) REVERT: B 782 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: B 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: B 965 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: C 233 ASP cc_start: 0.5927 (m-30) cc_final: 0.5720 (m-30) REVERT: C 277 GLU cc_start: 0.6190 (pm20) cc_final: 0.5896 (tt0) REVERT: C 546 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7250 (mp) REVERT: C 610 ASP cc_start: 0.6196 (p0) cc_final: 0.5926 (p0) REVERT: C 611 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.4046 (ptp-170) REVERT: C 745 MET cc_start: 0.3337 (tpt) cc_final: 0.3014 (tpp) REVERT: C 782 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: C 934 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: C 965 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: D 233 ASP cc_start: 0.5928 (m-30) cc_final: 0.5719 (m-30) REVERT: D 277 GLU cc_start: 0.6192 (pm20) cc_final: 0.5898 (tt0) REVERT: D 546 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7254 (mp) REVERT: D 610 ASP cc_start: 0.6196 (p0) cc_final: 0.5925 (p0) REVERT: D 611 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.4045 (ptp-170) REVERT: D 745 MET cc_start: 0.3339 (tpt) cc_final: 0.3008 (tpp) REVERT: D 782 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: D 934 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: D 965 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7535 (tm-30) outliers start: 180 outliers final: 120 residues processed: 592 average time/residue: 1.5546 time to fit residues: 1089.3955 Evaluate side-chains 584 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 444 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 50.0000 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 266 GLN A 485 GLN A 573 GLN A 761 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 485 GLN B 573 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 485 GLN C 573 GLN C 761 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 485 GLN D 573 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33876 Z= 0.209 Angle : 0.633 9.857 46216 Z= 0.321 Chirality : 0.044 0.148 4840 Planarity : 0.005 0.040 6092 Dihedral : 5.313 72.425 4580 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 4.52 % Allowed : 17.33 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4080 helix: -0.66 (0.22), residues: 552 sheet: 0.22 (0.14), residues: 1352 loop : -0.78 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 553 HIS 0.010 0.001 HIS C 30 PHE 0.016 0.002 PHE C 33 TYR 0.016 0.002 TYR C 100 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 456 time to evaluate : 3.667 Fit side-chains REVERT: A 52 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7127 (ttm-80) REVERT: A 233 ASP cc_start: 0.5928 (m-30) cc_final: 0.5705 (m-30) REVERT: A 277 GLU cc_start: 0.6179 (pm20) cc_final: 0.5889 (tt0) REVERT: A 546 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 610 ASP cc_start: 0.6165 (p0) cc_final: 0.5894 (p0) REVERT: A 611 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.4153 (ptp-170) REVERT: A 677 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7014 (ptpp) REVERT: A 745 MET cc_start: 0.3249 (tpt) cc_final: 0.2914 (tpp) REVERT: A 782 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: A 934 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: A 965 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: B 52 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7138 (ttm-80) REVERT: B 233 ASP cc_start: 0.5926 (m-30) cc_final: 0.5705 (m-30) REVERT: B 277 GLU cc_start: 0.6179 (pm20) cc_final: 0.5892 (tt0) REVERT: B 546 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7258 (mp) REVERT: B 610 ASP cc_start: 0.6167 (p0) cc_final: 0.5895 (p0) REVERT: B 611 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.4154 (ptp-170) REVERT: B 677 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7011 (ptpp) REVERT: B 745 MET cc_start: 0.3255 (tpt) cc_final: 0.2913 (tpp) REVERT: B 782 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: B 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: B 965 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: C 52 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7128 (ttm-80) REVERT: C 233 ASP cc_start: 0.5926 (m-30) cc_final: 0.5705 (m-30) REVERT: C 277 GLU cc_start: 0.6179 (pm20) cc_final: 0.5889 (tt0) REVERT: C 546 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7260 (mp) REVERT: C 610 ASP cc_start: 0.6167 (p0) cc_final: 0.5896 (p0) REVERT: C 611 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.4153 (ptp-170) REVERT: C 677 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7013 (ptpp) REVERT: C 745 MET cc_start: 0.3250 (tpt) cc_final: 0.2914 (tpp) REVERT: C 782 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: C 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: C 965 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: D 52 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7138 (ttm-80) REVERT: D 233 ASP cc_start: 0.5927 (m-30) cc_final: 0.5704 (m-30) REVERT: D 277 GLU cc_start: 0.6179 (pm20) cc_final: 0.5890 (tt0) REVERT: D 546 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7263 (mp) REVERT: D 610 ASP cc_start: 0.6166 (p0) cc_final: 0.5895 (p0) REVERT: D 611 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.4152 (ptp-170) REVERT: D 677 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7014 (ptpp) REVERT: D 745 MET cc_start: 0.3254 (tpt) cc_final: 0.2918 (tpp) REVERT: D 782 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: D 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: D 965 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7526 (tm-30) outliers start: 158 outliers final: 104 residues processed: 572 average time/residue: 1.6651 time to fit residues: 1120.7694 Evaluate side-chains 552 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 420 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 0.1980 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 0.0370 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 485 GLN A 573 GLN A 624 GLN A 824 GLN A 878 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 485 GLN B 573 GLN B 624 GLN B 824 GLN B 878 HIS ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 485 GLN C 573 GLN C 624 GLN C 824 GLN C 878 HIS ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 485 GLN D 573 GLN D 624 GLN D 824 GLN D 878 HIS ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33876 Z= 0.164 Angle : 0.582 9.533 46216 Z= 0.295 Chirality : 0.043 0.147 4840 Planarity : 0.004 0.038 6092 Dihedral : 5.032 71.210 4580 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 3.69 % Allowed : 18.39 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4080 helix: -0.47 (0.23), residues: 548 sheet: 0.31 (0.14), residues: 1352 loop : -0.73 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 553 HIS 0.011 0.001 HIS D 30 PHE 0.018 0.001 PHE A 33 TYR 0.014 0.001 TYR A 100 ARG 0.005 0.000 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 466 time to evaluate : 3.847 Fit side-chains REVERT: A 77 ASP cc_start: 0.6524 (p0) cc_final: 0.6278 (p0) REVERT: A 277 GLU cc_start: 0.6174 (pm20) cc_final: 0.5859 (tt0) REVERT: A 610 ASP cc_start: 0.6150 (p0) cc_final: 0.5941 (p0) REVERT: A 611 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.4205 (ptp-170) REVERT: A 745 MET cc_start: 0.3184 (tpt) cc_final: 0.2876 (tpp) REVERT: A 782 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: A 934 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: A 965 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 77 ASP cc_start: 0.6525 (p0) cc_final: 0.6280 (p0) REVERT: B 277 GLU cc_start: 0.6171 (pm20) cc_final: 0.5855 (tt0) REVERT: B 610 ASP cc_start: 0.6148 (p0) cc_final: 0.5940 (p0) REVERT: B 611 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.4204 (ptp-170) REVERT: B 745 MET cc_start: 0.3200 (tpt) cc_final: 0.2886 (tpp) REVERT: B 782 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: B 934 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: B 965 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: C 77 ASP cc_start: 0.6524 (p0) cc_final: 0.6278 (p0) REVERT: C 277 GLU cc_start: 0.6173 (pm20) cc_final: 0.5857 (tt0) REVERT: C 610 ASP cc_start: 0.6149 (p0) cc_final: 0.5936 (p0) REVERT: C 611 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.4211 (ptp-170) REVERT: C 745 MET cc_start: 0.3186 (tpt) cc_final: 0.2877 (tpp) REVERT: C 782 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: C 934 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6661 (tp30) REVERT: C 965 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: D 77 ASP cc_start: 0.6524 (p0) cc_final: 0.6279 (p0) REVERT: D 277 GLU cc_start: 0.6172 (pm20) cc_final: 0.5856 (tt0) REVERT: D 610 ASP cc_start: 0.6147 (p0) cc_final: 0.5938 (p0) REVERT: D 611 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.4203 (ptp-170) REVERT: D 745 MET cc_start: 0.3186 (tpt) cc_final: 0.2877 (tpp) REVERT: D 782 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: D 934 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: D 965 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7508 (tm-30) outliers start: 129 outliers final: 72 residues processed: 570 average time/residue: 1.5780 time to fit residues: 1062.9552 Evaluate side-chains 521 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 433 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 0.4980 chunk 198 optimal weight: 0.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 30 HIS A 262 GLN A 485 GLN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 30 HIS B 262 GLN B 485 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 30 HIS C 262 GLN C 485 GLN C 824 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 30 HIS D 262 GLN D 485 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33876 Z= 0.230 Angle : 0.644 9.727 46216 Z= 0.327 Chirality : 0.045 0.145 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.296 72.558 4580 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 3.23 % Allowed : 18.91 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4080 helix: -0.54 (0.23), residues: 548 sheet: 0.38 (0.15), residues: 1268 loop : -0.85 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 553 HIS 0.012 0.001 HIS C 30 PHE 0.018 0.002 PHE B 33 TYR 0.016 0.002 TYR C 100 ARG 0.005 0.001 ARG A 857 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 448 time to evaluate : 3.926 Fit side-chains REVERT: A 77 ASP cc_start: 0.6503 (p0) cc_final: 0.6267 (p0) REVERT: A 277 GLU cc_start: 0.6167 (pm20) cc_final: 0.5880 (tt0) REVERT: A 610 ASP cc_start: 0.6168 (p0) cc_final: 0.5925 (p0) REVERT: A 611 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.4074 (ptp-170) REVERT: A 745 MET cc_start: 0.3269 (tpt) cc_final: 0.2958 (tpp) REVERT: A 782 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: A 934 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: A 965 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: B 77 ASP cc_start: 0.6504 (p0) cc_final: 0.6269 (p0) REVERT: B 277 GLU cc_start: 0.6164 (pm20) cc_final: 0.5878 (tt0) REVERT: B 610 ASP cc_start: 0.6166 (p0) cc_final: 0.5923 (p0) REVERT: B 611 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.4075 (ptp-170) REVERT: B 745 MET cc_start: 0.3266 (tpt) cc_final: 0.2956 (tpp) REVERT: B 782 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: B 934 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: B 965 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: C 77 ASP cc_start: 0.6502 (p0) cc_final: 0.6267 (p0) REVERT: C 277 GLU cc_start: 0.6166 (pm20) cc_final: 0.5880 (tt0) REVERT: C 610 ASP cc_start: 0.6163 (p0) cc_final: 0.5921 (p0) REVERT: C 611 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.4081 (ptp-170) REVERT: C 745 MET cc_start: 0.3268 (tpt) cc_final: 0.2957 (tpp) REVERT: C 782 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: C 934 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6721 (tp30) REVERT: C 965 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: D 77 ASP cc_start: 0.6503 (p0) cc_final: 0.6268 (p0) REVERT: D 277 GLU cc_start: 0.6166 (pm20) cc_final: 0.5879 (tt0) REVERT: D 610 ASP cc_start: 0.6167 (p0) cc_final: 0.5925 (p0) REVERT: D 611 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.4058 (ptp-170) REVERT: D 745 MET cc_start: 0.3268 (tpt) cc_final: 0.2958 (tpp) REVERT: D 782 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: D 934 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: D 965 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7511 (tm-30) outliers start: 113 outliers final: 75 residues processed: 540 average time/residue: 1.6132 time to fit residues: 1029.0642 Evaluate side-chains 529 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 438 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 871 GLU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 748 CYS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 1004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 262 GLN A 395 HIS A 485 GLN A 824 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 395 HIS B 485 GLN B 824 GLN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 395 HIS C 485 GLN C 824 GLN ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 395 HIS D 485 GLN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149919 restraints weight = 33682.919| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.21 r_work: 0.3663 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33876 Z= 0.231 Angle : 0.647 9.815 46216 Z= 0.328 Chirality : 0.045 0.145 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.346 73.811 4580 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 3.66 % Allowed : 19.08 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4080 helix: -0.58 (0.22), residues: 552 sheet: 0.36 (0.14), residues: 1304 loop : -0.82 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 553 HIS 0.011 0.001 HIS B 30 PHE 0.017 0.002 PHE B 33 TYR 0.017 0.002 TYR C1014 ARG 0.006 0.001 ARG C 857 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16166.54 seconds wall clock time: 284 minutes 46.13 seconds (17086.13 seconds total)