Starting phenix.real_space_refine on Sat Dec 16 02:50:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/12_2023/5a1a_2984_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/12_2023/5a1a_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_2984/12_2023/5a1a_2984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/12_2023/5a1a_2984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/12_2023/5a1a_2984_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a1a_2984/12_2023/5a1a_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.85, 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: 13.20 Conformation dependent library (CDL) restraints added in 5.8 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: 8.73 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: 16.54 Time building geometry restraints manager: 14.12 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: 0.010 Normalize map: mean=0, sd=1: 1.320 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: 0.030 Extract box with map and model: 7.520 Check model and map are aligned: 0.500 Set scattering table: 0.260 Process input model: 90.980 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.530 ------------------------------------------------------------------------------- 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 : 3.586 Fit side-chains outliers start: 36 outliers final: 4 residues processed: 812 average time/residue: 1.5881 time to fit residues: 1525.2954 Evaluate side-chains 504 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 500 time to evaluate : 3.638 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.3090 time to fit residues: 11.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 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 896 ASN B 935 ASN B 985 ASN B1015 HIS 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 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 896 ASN D 935 ASN D 985 ASN D1015 HIS Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2079 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= 0.219 Angle : 0.646 9.894 46216 Z= 0.333 Chirality : 0.045 0.156 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.121 65.853 4580 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 3.43 % Allowed : 13.73 % Favored : 82.84 % 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: -0.96 (0.12), residues: 4080 helix: -1.24 (0.21), residues: 564 sheet: 0.06 (0.14), residues: 1344 loop : -0.88 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 90 HIS 0.007 0.001 HIS C 395 PHE 0.012 0.002 PHE D 63 TYR 0.013 0.002 TYR B 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 648 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 528 time to evaluate : 3.893 Fit side-chains outliers start: 120 outliers final: 48 residues processed: 604 average time/residue: 1.6647 time to fit residues: 1190.9802 Evaluate side-chains 504 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 456 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 40 residues processed: 8 average time/residue: 1.1242 time to fit residues: 16.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- 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 554 GLN A 573 GLN A 583 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 791 ASN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 554 GLN B 573 GLN B 583 ASN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN B 791 ASN ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 554 GLN C 573 GLN C 583 ASN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 GLN C 791 ASN ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 554 GLN D 573 GLN D 583 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 783 GLN D 791 ASN ** D 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33876 Z= 0.414 Angle : 0.816 10.521 46216 Z= 0.423 Chirality : 0.051 0.164 4840 Planarity : 0.007 0.064 6092 Dihedral : 5.892 69.283 4580 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 5.61 % Allowed : 14.07 % Favored : 80.32 % 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: -0.97 (0.12), residues: 4080 helix: -1.24 (0.21), residues: 552 sheet: -0.00 (0.13), residues: 1416 loop : -0.86 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 553 HIS 0.008 0.002 HIS C 464 PHE 0.021 0.003 PHE A 63 TYR 0.023 0.003 TYR D 123 ARG 0.007 0.001 ARG D 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 676 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 480 time to evaluate : 3.688 Fit side-chains outliers start: 196 outliers final: 96 residues processed: 620 average time/residue: 1.6615 time to fit residues: 1216.4354 Evaluate side-chains 548 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 452 time to evaluate : 4.660 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 80 residues processed: 16 average time/residue: 1.5925 time to fit residues: 35.8800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 485 GLN A 510 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 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 266 GLN B 485 GLN B 510 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 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 266 GLN C 485 GLN C 510 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 485 GLN D 510 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2845 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= 0.237 Angle : 0.668 10.244 46216 Z= 0.340 Chirality : 0.045 0.157 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.465 71.074 4580 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 4.75 % Allowed : 15.27 % Favored : 79.98 % 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: -0.78 (0.13), residues: 4080 helix: -0.98 (0.22), residues: 548 sheet: 0.20 (0.14), residues: 1360 loop : -0.81 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 553 HIS 0.007 0.001 HIS C 30 PHE 0.012 0.002 PHE D 63 TYR 0.016 0.002 TYR B 100 ARG 0.004 0.001 ARG A 611 *********************** 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 634 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 468 time to evaluate : 3.717 Fit side-chains outliers start: 166 outliers final: 112 residues processed: 602 average time/residue: 1.6294 time to fit residues: 1165.2813 Evaluate side-chains 544 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 432 time to evaluate : 3.697 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 100 residues processed: 12 average time/residue: 0.9709 time to fit residues: 20.5919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 272 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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 485 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 485 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 485 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2892 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= 0.221 Angle : 0.642 9.584 46216 Z= 0.327 Chirality : 0.045 0.157 4840 Planarity : 0.005 0.042 6092 Dihedral : 5.338 70.916 4580 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 4.89 % Allowed : 15.59 % Favored : 79.52 % 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: -0.81 (0.22), residues: 548 sheet: 0.24 (0.14), residues: 1352 loop : -0.78 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 553 HIS 0.007 0.001 HIS B 30 PHE 0.011 0.002 PHE C 63 TYR 0.016 0.002 TYR D 100 ARG 0.005 0.001 ARG D 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 623 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 452 time to evaluate : 3.730 Fit side-chains outliers start: 171 outliers final: 100 residues processed: 587 average time/residue: 1.5483 time to fit residues: 1086.6889 Evaluate side-chains 556 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 456 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 84 residues processed: 16 average time/residue: 0.6455 time to fit residues: 20.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.0050 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 394 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 30 HIS A 262 GLN A 266 GLN A 485 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 12 GLN B 30 HIS B 262 GLN B 266 GLN B 485 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 12 GLN C 30 HIS C 262 GLN C 266 GLN C 485 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 12 GLN D 30 HIS D 262 GLN D 266 GLN D 485 GLN D 775 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3009 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= 0.223 Angle : 0.643 9.326 46216 Z= 0.327 Chirality : 0.045 0.155 4840 Planarity : 0.005 0.041 6092 Dihedral : 5.350 71.020 4580 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 4.83 % Allowed : 15.99 % Favored : 79.18 % 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: -0.68 (0.13), residues: 4080 helix: -0.74 (0.22), residues: 548 sheet: 0.26 (0.14), residues: 1352 loop : -0.79 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 553 HIS 0.008 0.001 HIS D 30 PHE 0.012 0.002 PHE D 63 TYR 0.016 0.002 TYR B 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 669 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 500 time to evaluate : 4.455 Fit side-chains outliers start: 169 outliers final: 101 residues processed: 625 average time/residue: 1.5629 time to fit residues: 1169.7814 Evaluate side-chains 561 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 460 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 93 residues processed: 8 average time/residue: 0.4001 time to fit residues: 10.6811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.4980 chunk 44 optimal weight: 20.0000 chunk 224 optimal weight: 30.0000 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 0.0770 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- 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 624 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 262 GLN B 266 GLN B 485 GLN B 624 GLN ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 HIS ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 262 GLN C 266 GLN C 485 GLN C 624 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 878 HIS ** C 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 262 GLN D 266 GLN D 485 GLN D 624 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33876 Z= 0.142 Angle : 0.561 9.357 46216 Z= 0.283 Chirality : 0.042 0.137 4840 Planarity : 0.004 0.037 6092 Dihedral : 4.906 69.375 4580 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 4.26 % Allowed : 17.33 % Favored : 78.40 % 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: -0.49 (0.13), residues: 4080 helix: -0.49 (0.23), residues: 548 sheet: 0.40 (0.14), residues: 1340 loop : -0.70 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 553 HIS 0.008 0.001 HIS C 30 PHE 0.013 0.001 PHE D 33 TYR 0.013 0.001 TYR D 100 ARG 0.007 0.000 ARG B 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 624 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 475 time to evaluate : 3.707 Fit side-chains outliers start: 149 outliers final: 84 residues processed: 596 average time/residue: 1.5948 time to fit residues: 1133.6800 Evaluate side-chains 531 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 447 time to evaluate : 4.149 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 84 residues processed: 4 average time/residue: 1.4439 time to fit residues: 12.6133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 0.0870 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 267 optimal weight: 0.5980 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 309 optimal weight: 0.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- 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 266 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 18 ASN B 30 HIS B 266 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 18 ASN C 30 HIS C 266 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 18 ASN D 30 HIS D 266 GLN D 395 HIS D 485 GLN D 775 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 33876 Z= 0.153 Angle : 0.564 9.122 46216 Z= 0.285 Chirality : 0.043 0.135 4840 Planarity : 0.004 0.038 6092 Dihedral : 4.850 68.360 4580 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.82 % Rotamer: Outliers : 4.41 % Allowed : 17.42 % Favored : 78.18 % 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: -0.38 (0.13), residues: 4080 helix: -0.39 (0.23), residues: 548 sheet: 0.46 (0.14), residues: 1356 loop : -0.63 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 553 HIS 0.008 0.001 HIS C 30 PHE 0.007 0.001 PHE C 758 TYR 0.013 0.001 TYR C 100 ARG 0.006 0.000 ARG B 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 622 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 468 time to evaluate : 3.679 Fit side-chains outliers start: 154 outliers final: 89 residues processed: 598 average time/residue: 1.5545 time to fit residues: 1111.4893 Evaluate side-chains 526 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 437 time to evaluate : 3.797 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 85 residues processed: 4 average time/residue: 0.3090 time to fit residues: 7.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.8980 chunk 376 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 40.0000 chunk 112 optimal weight: 0.4980 chunk 331 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 0.7980 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 266 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 266 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 266 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 266 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33876 Z= 0.177 Angle : 0.593 9.212 46216 Z= 0.299 Chirality : 0.044 0.139 4840 Planarity : 0.004 0.040 6092 Dihedral : 4.949 69.118 4580 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 3.43 % Allowed : 18.74 % Favored : 77.83 % 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: -0.39 (0.13), residues: 4080 helix: -0.42 (0.23), residues: 548 sheet: 0.44 (0.14), residues: 1348 loop : -0.62 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 553 HIS 0.009 0.001 HIS A 30 PHE 0.017 0.001 PHE C 33 TYR 0.014 0.002 TYR B 100 ARG 0.006 0.000 ARG C 857 *********************** 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 572 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 452 time to evaluate : 5.727 Fit side-chains outliers start: 120 outliers final: 83 residues processed: 556 average time/residue: 1.6237 time to fit residues: 1080.2579 Evaluate side-chains 508 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 425 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 83 residues processed: 0 time to fit residues: 5.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 151 HIS A 266 GLN A 485 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 151 HIS B 266 GLN B 485 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 151 HIS C 266 GLN C 485 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 151 HIS D 266 GLN D 485 GLN D 824 GLN ** D 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33876 Z= 0.311 Angle : 0.716 8.831 46216 Z= 0.366 Chirality : 0.048 0.163 4840 Planarity : 0.005 0.059 6092 Dihedral : 5.546 73.716 4580 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 4.06 % Allowed : 18.68 % 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: -0.61 (0.13), residues: 4080 helix: -0.69 (0.22), residues: 552 sheet: 0.43 (0.14), residues: 1300 loop : -0.80 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 553 HIS 0.008 0.002 HIS B 30 PHE 0.020 0.002 PHE D 33 TYR 0.019 0.002 TYR B 100 ARG 0.010 0.001 ARG C 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 593 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 451 time to evaluate : 3.775 Fit side-chains outliers start: 142 outliers final: 95 residues processed: 571 average time/residue: 1.6508 time to fit residues: 1119.1803 Evaluate side-chains 532 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 437 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 91 residues processed: 4 average time/residue: 0.3089 time to fit residues: 7.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 266 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 30 HIS B 266 GLN 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 266 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 30 HIS D 245 GLN D 266 GLN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150817 restraints weight = 33649.383| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.21 r_work: 0.3673 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3160 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= 0.194 Angle : 0.619 8.734 46216 Z= 0.313 Chirality : 0.044 0.139 4840 Planarity : 0.004 0.037 6092 Dihedral : 5.227 73.248 4580 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 2.92 % Allowed : 19.54 % Favored : 77.55 % 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: -0.53 (0.13), residues: 4080 helix: -0.58 (0.22), residues: 548 sheet: 0.43 (0.14), residues: 1340 loop : -0.75 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 553 HIS 0.007 0.001 HIS B 30 PHE 0.015 0.001 PHE B 33 TYR 0.015 0.002 TYR D 100 ARG 0.008 0.000 ARG A 857 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16344.30 seconds wall clock time: 289 minutes 14.47 seconds (17354.47 seconds total)