Starting phenix.real_space_refine on Sat Mar 23 13:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cvm_7770/03_2024/6cvm_7770_updated.pdb" } resolution = 1.9 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= -0.008 sd= 0.159 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 20792 2.51 5 N 5800 2.21 5 O 10294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "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 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" 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 ARG 561": "NH1" <-> "NH2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 952": "NH1" <-> "NH2" Residue "A PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "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 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 438": "OE1" <-> "OE2" 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 ARG 561": "NH1" <-> "NH2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 952": "NH1" <-> "NH2" Residue "B PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 1013": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "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 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 438": "OE1" <-> "OE2" 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 ARG 561": "NH1" <-> "NH2" Residue "C TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 699": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 952": "NH1" <-> "NH2" Residue "C PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 1013": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 190": "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 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 438": "OE1" <-> "OE2" 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 ARG 561": "NH1" <-> "NH2" Residue "D TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 699": "NH1" <-> "NH2" Residue "D ARG 721": "NH1" <-> "NH2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 952": "NH1" <-> "NH2" Residue "D PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 961": "NH1" <-> "NH2" Residue "D ARG 1013": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37062 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8193 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} Chain: "B" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8193 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} Chain: "C" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8193 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} Chain: "D" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8193 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} 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: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 1047 Classifications: {'water': 1047} Link IDs: {None: 1046} Chain: "B" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 1048 Classifications: {'water': 1048} Link IDs: {None: 1047} Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 1050 Classifications: {'water': 1050} Link IDs: {None: 1049} Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 1049 Classifications: {'water': 1049} Link IDs: {None: 1048} Time building chain proxies: 20.08, per 1000 atoms: 0.54 Number of scatterers: 37062 At special positions: 0 Unit cell: (191.737, 150.969, 100.009, 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 10294 8.00 N 5800 7.00 C 20792 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: 15.43 Conformation dependent library (CDL) restraints added in 5.6 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 52 sheets defined 13.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 10 No H-bonds generated for 'chain 'A' and resid 7 through 10' Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' 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 74 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.812A pdb=" N GLN A 135 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.766A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.604A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.597A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 4.008A 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 Processing helix chain 'A' and resid 599 through 602 removed outlier: 3.995A 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 615 through 623 removed outlier: 3.583A pdb=" N GLN A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) 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 812 Processing helix chain 'A' and resid 922 through 925 Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' 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 74 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.812A pdb=" N GLN B 135 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 396 through 405 removed outlier: 3.766A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.604A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.597A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.008A 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 Processing helix chain 'B' and resid 599 through 602 removed outlier: 3.994A 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 615 through 623 removed outlier: 3.584A pdb=" N GLN B 623 " --> pdb=" O ALA B 620 " (cutoff:3.500A) 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 812 Processing helix chain 'B' and resid 922 through 925 Processing helix chain 'B' and resid 964 through 969 Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 1005 through 1007 No H-bonds generated for 'chain 'B' and resid 1005 through 1007' Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' 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 74 Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.812A pdb=" N GLN C 135 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 396 through 405 removed outlier: 3.766A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 removed outlier: 3.604A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.597A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.008A 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 Processing helix chain 'C' and resid 599 through 602 removed outlier: 3.994A 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 615 through 623 removed outlier: 3.584A pdb=" N GLN C 623 " --> pdb=" O ALA C 620 " (cutoff:3.500A) 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 812 Processing helix chain 'C' and resid 922 through 925 Processing helix chain 'C' and resid 964 through 969 Processing helix chain 'C' and resid 973 through 975 No H-bonds generated for 'chain 'C' and resid 973 through 975' Processing helix chain 'C' and resid 1005 through 1007 No H-bonds generated for 'chain 'C' and resid 1005 through 1007' Processing helix chain 'D' and resid 7 through 10 No H-bonds generated for 'chain 'D' and resid 7 through 10' Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' 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 74 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.812A pdb=" N GLN D 135 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.766A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.604A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 478 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.597A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.008A 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 Processing helix chain 'D' and resid 599 through 602 removed outlier: 3.996A 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 615 through 623 removed outlier: 3.583A pdb=" N GLN D 623 " --> pdb=" O ALA D 620 " (cutoff:3.500A) 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 812 Processing helix chain 'D' and resid 922 through 925 Processing helix chain 'D' and resid 964 through 969 Processing helix chain 'D' and resid 973 through 975 No H-bonds generated for 'chain 'D' and resid 973 through 975' Processing helix chain 'D' and resid 1005 through 1007 No H-bonds generated for 'chain 'D' and resid 1005 through 1007' 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: 8.562A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS A 154 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 5.381A 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: 4.069A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 288 through 296 removed outlier: 6.040A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.683A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (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: 5.948A pdb=" N ILE A 351 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 567 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY A 353 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 386 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG A 356 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG A 388 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 408 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS A 389 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 410 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP A 411 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.562A 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 632 Processing sheet with id= J, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.682A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.007A 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: 6.752A pdb=" N LEU A 884 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP A 987 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 886 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN A 985 " --> pdb=" O CYS A 886 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 888 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 5.424A 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: 6.572A pdb=" N TRP A 842 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 851 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS A 840 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG A 853 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 838 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 855 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 836 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 857 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 834 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.136A 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: 8.563A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS B 154 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 5.381A 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: 4.069A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 288 through 296 removed outlier: 6.040A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.683A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (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: 5.948A pdb=" N ILE B 351 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B 567 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY B 353 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 386 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG B 356 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG B 388 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 408 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS B 389 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL B 410 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP B 411 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.563A 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 632 Processing sheet with id= W, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.683A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.007A 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: 6.753A pdb=" N LEU B 884 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP B 987 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N CYS B 886 " --> pdb=" O ASN B 985 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN B 985 " --> pdb=" O CYS B 886 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 888 " --> pdb=" O TRP B 983 " (cutoff:3.500A) removed outlier: 5.424A 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: 6.572A pdb=" N TRP B 842 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE B 851 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS B 840 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 853 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 838 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 855 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 836 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG B 857 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 834 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.136A 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: 8.562A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS C 154 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 5.381A 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: 4.069A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 288 through 296 removed outlier: 6.040A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.684A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (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: 5.948A pdb=" N ILE C 351 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL C 567 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY C 353 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 386 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG C 356 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG C 388 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR C 408 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS C 389 " --> pdb=" O TYR C 408 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 410 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 411 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.562A 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 632 Processing sheet with id= AJ, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.682A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.007A 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: 6.753A pdb=" N LEU C 884 " --> pdb=" O ASP C 987 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 987 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS C 886 " --> pdb=" O ASN C 985 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN C 985 " --> pdb=" O CYS C 886 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 888 " --> pdb=" O TRP C 983 " (cutoff:3.500A) removed outlier: 5.424A 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: 6.572A pdb=" N TRP C 842 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 851 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS C 840 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG C 853 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 838 " --> pdb=" O ARG C 853 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 855 " --> pdb=" O ILE C 836 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 836 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG C 857 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 834 " --> pdb=" O ARG C 857 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.136A 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: 8.562A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS D 154 " --> pdb=" O TRP D 158 " (cutoff:3.500A) removed outlier: 5.381A 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: 4.069A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 288 through 296 removed outlier: 6.040A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.683A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (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: 5.949A pdb=" N ILE D 351 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL D 567 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY D 353 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 386 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ARG D 356 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG D 388 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR D 408 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS D 389 " --> pdb=" O TYR D 408 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D 410 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP D 411 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.561A 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 632 Processing sheet with id= AW, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.682A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.007A 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: 6.753A pdb=" N LEU D 884 " --> pdb=" O ASP D 987 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP D 987 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS D 886 " --> pdb=" O ASN D 985 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN D 985 " --> pdb=" O CYS D 886 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 888 " --> pdb=" O TRP D 983 " (cutoff:3.500A) removed outlier: 5.424A 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: 6.573A pdb=" N TRP D 842 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE D 851 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS D 840 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 853 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 838 " --> pdb=" O ARG D 853 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 855 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 836 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG D 857 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL D 834 " --> pdb=" O ARG D 857 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2496 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: 19.62 Time building geometry restraints manager: 16.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5576 1.31 - 1.44: 9779 1.44 - 1.56: 18213 1.56 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 33824 Sorted by residual: bond pdb=" C13 PTQ B2001 " pdb=" C14 PTQ B2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ C2001 " pdb=" C14 PTQ C2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ A2001 " pdb=" C14 PTQ A2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ D2001 " pdb=" C14 PTQ D2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C11 PTQ D2001 " pdb=" C12 PTQ D2001 " ideal model delta sigma weight residual 1.389 1.510 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 33819 not shown) Histogram of bond angle deviations from ideal: 96.48 - 104.01: 642 104.01 - 111.55: 14706 111.55 - 119.08: 12364 119.08 - 126.62: 17518 126.62 - 134.15: 926 Bond angle restraints: 46156 Sorted by residual: angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" CB VAL A 334 " ideal model delta sigma weight residual 111.52 118.22 -6.70 1.46e+00 4.69e-01 2.10e+01 angle pdb=" C PRO A 513 " pdb=" N ALA A 514 " pdb=" CA ALA A 514 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C PRO B 513 " pdb=" N ALA B 514 " pdb=" CA ALA B 514 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" N VAL D 334 " pdb=" CA VAL D 334 " pdb=" CB VAL D 334 " ideal model delta sigma weight residual 111.52 118.19 -6.67 1.46e+00 4.69e-01 2.09e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 111.52 118.19 -6.67 1.46e+00 4.69e-01 2.09e+01 ... (remaining 46151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 18759 15.58 - 31.15: 873 31.15 - 46.73: 180 46.73 - 62.30: 44 62.30 - 77.88: 8 Dihedral angle restraints: 19864 sinusoidal: 8060 harmonic: 11804 Sorted by residual: dihedral pdb=" CA PHE D 957 " pdb=" C PHE D 957 " pdb=" N ASN D 958 " pdb=" CA ASN D 958 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE C 957 " pdb=" C PHE C 957 " pdb=" N ASN C 958 " pdb=" CA ASN C 958 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE B 957 " pdb=" C PHE B 957 " pdb=" N ASN B 958 " pdb=" CA ASN B 958 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3179 0.060 - 0.119: 1395 0.119 - 0.179: 226 0.179 - 0.239: 25 0.239 - 0.298: 19 Chirality restraints: 4844 Sorted by residual: chirality pdb=" CB ILE A 959 " pdb=" CA ILE A 959 " pdb=" CG1 ILE A 959 " pdb=" CG2 ILE A 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE C 959 " pdb=" CA ILE C 959 " pdb=" CG1 ILE C 959 " pdb=" CG2 ILE C 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE D 959 " pdb=" CA ILE D 959 " pdb=" CG1 ILE D 959 " pdb=" CG2 ILE D 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4841 not shown) Planarity restraints: 6080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1020 " 0.026 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP D1020 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP D1020 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D1020 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D1020 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D1020 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D1020 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1020 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D1020 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1020 " 0.027 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" CG TRP B1020 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP B1020 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B1020 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B1020 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B1020 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1020 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1020 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1020 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP C1020 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C1020 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C1020 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C1020 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C1020 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1020 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1020 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1020 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C1020 " -0.002 2.00e-02 2.50e+03 ... (remaining 6077 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 2187 2.62 - 3.19: 31906 3.19 - 3.76: 69284 3.76 - 4.33: 103102 4.33 - 4.90: 156294 Nonbonded interactions: 362773 Sorted by model distance: nonbonded pdb=" OE1 GLU A 461 " pdb="MG MG A2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU B 461 " pdb="MG MG B2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU C 461 " pdb="MG MG C2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU D 461 " pdb="MG MG D2002 " model vdw 2.053 2.170 nonbonded pdb="MG MG D2002 " pdb=" O HOH D2225 " model vdw 2.066 2.170 ... (remaining 362768 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: 1.600 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: 10.080 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 103.480 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.210 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 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 : 0.012 0.125 33824 Z= 0.772 Angle : 0.924 10.521 46156 Z= 0.505 Chirality : 0.065 0.298 4844 Planarity : 0.007 0.055 6080 Dihedral : 10.251 77.881 12264 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -1.16 (0.12), residues: 4076 helix: -2.82 (0.16), residues: 500 sheet: 0.08 (0.13), residues: 1396 loop : -0.77 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.005 TRP D1020 HIS 0.014 0.003 HIS A 464 PHE 0.020 0.003 PHE C 747 TYR 0.043 0.004 TYR D 559 ARG 0.014 0.002 ARG C 881 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 4.356 Fit side-chains REVERT: A 82 ASP cc_start: 0.7820 (m-30) cc_final: 0.7509 (m-30) REVERT: A 804 ASN cc_start: 0.8872 (m110) cc_final: 0.8669 (m-40) REVERT: B 82 ASP cc_start: 0.7814 (m-30) cc_final: 0.7509 (m-30) REVERT: B 117 GLU cc_start: 0.7442 (pm20) cc_final: 0.7235 (pm20) REVERT: C 82 ASP cc_start: 0.7821 (m-30) cc_final: 0.7507 (m-30) REVERT: C 804 ASN cc_start: 0.8875 (m110) cc_final: 0.8670 (m-40) REVERT: D 82 ASP cc_start: 0.7819 (m-30) cc_final: 0.7510 (m-30) REVERT: D 804 ASN cc_start: 0.8881 (m110) cc_final: 0.8670 (m-40) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 1.9478 time to fit residues: 994.1044 Evaluate side-chains 336 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 4.056 ------------------------------------------------------------------------------- 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: 4.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 370 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 266 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 863 GLN A 935 ASN A 966 GLN B 12 GLN B 266 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 646 HIS B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 863 GLN B 935 ASN B 966 GLN C 12 GLN C 266 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 GLN C 863 GLN C 935 ASN C 965 GLN C 966 GLN D 12 GLN D 266 GLN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 GLN D 863 GLN D 935 ASN D 966 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33824 Z= 0.208 Angle : 0.574 10.420 46156 Z= 0.300 Chirality : 0.045 0.161 4844 Planarity : 0.004 0.036 6080 Dihedral : 6.127 59.334 4576 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 4.44 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -0.30 (0.13), residues: 4076 helix: -1.21 (0.20), residues: 528 sheet: 0.47 (0.13), residues: 1364 loop : -0.28 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 553 HIS 0.004 0.001 HIS C 464 PHE 0.016 0.001 PHE B 549 TYR 0.019 0.002 TYR A 100 ARG 0.006 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 383 time to evaluate : 4.441 Fit side-chains REVERT: A 82 ASP cc_start: 0.7884 (m-30) cc_final: 0.7609 (m-30) REVERT: A 241 GLU cc_start: 0.7858 (tt0) cc_final: 0.7636 (tt0) REVERT: A 438 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 82 ASP cc_start: 0.7881 (m-30) cc_final: 0.7605 (m-30) REVERT: B 117 GLU cc_start: 0.7386 (pm20) cc_final: 0.7183 (pm20) REVERT: B 128 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (t0) REVERT: B 438 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7523 (mt-10) REVERT: C 82 ASP cc_start: 0.7886 (m-30) cc_final: 0.7611 (m-30) REVERT: C 438 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7531 (mt-10) REVERT: D 82 ASP cc_start: 0.7883 (m-30) cc_final: 0.7608 (m-30) REVERT: D 128 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (t0) REVERT: D 438 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7523 (mt-10) outliers start: 34 outliers final: 4 residues processed: 401 average time/residue: 1.8607 time to fit residues: 875.5839 Evaluate side-chains 351 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 345 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 515 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 563 GLN A 573 GLN A 622 HIS A 687 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 863 GLN A 945 ASN B 262 GLN B 563 GLN B 622 HIS B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 863 GLN B 945 ASN C 262 GLN C 563 GLN C 573 GLN C 622 HIS C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 945 ASN C 965 GLN D 262 GLN D 563 GLN D 573 GLN D 622 HIS D 687 GLN D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 GLN D 863 GLN D 945 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 33824 Z= 0.503 Angle : 0.667 10.699 46156 Z= 0.350 Chirality : 0.051 0.192 4844 Planarity : 0.005 0.037 6080 Dihedral : 6.343 58.107 4576 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.17 % Allowed : 6.27 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.15 (0.13), residues: 4076 helix: -0.78 (0.20), residues: 528 sheet: 0.73 (0.13), residues: 1396 loop : 0.01 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 553 HIS 0.007 0.002 HIS B 464 PHE 0.015 0.002 PHE D 989 TYR 0.024 0.002 TYR B 100 ARG 0.004 0.001 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 4.507 Fit side-chains REVERT: A 243 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 367 MET cc_start: 0.8992 (mmp) cc_final: 0.8720 (mmp) REVERT: A 843 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: B 128 ASN cc_start: 0.8425 (m110) cc_final: 0.8116 (t0) REVERT: B 243 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: B 367 MET cc_start: 0.8998 (mmp) cc_final: 0.8717 (mmp) REVERT: B 843 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: C 243 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: C 367 MET cc_start: 0.8994 (mmp) cc_final: 0.8728 (mmp) REVERT: C 843 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: D 128 ASN cc_start: 0.8422 (m110) cc_final: 0.8116 (t0) REVERT: D 243 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: D 367 MET cc_start: 0.8996 (mmp) cc_final: 0.8716 (mmp) REVERT: D 843 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8363 (mt0) outliers start: 41 outliers final: 20 residues processed: 377 average time/residue: 1.9019 time to fit residues: 841.8751 Evaluate side-chains 362 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 843 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 843 GLN Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS A 761 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS A 863 GLN B 739 HIS B 761 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS B 863 GLN C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 HIS C 863 GLN D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 HIS D 863 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33824 Z= 0.155 Angle : 0.520 10.871 46156 Z= 0.269 Chirality : 0.044 0.162 4844 Planarity : 0.003 0.029 6080 Dihedral : 5.745 59.800 4576 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.06 % Allowed : 6.73 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.33 (0.13), residues: 4076 helix: -0.30 (0.22), residues: 528 sheet: 0.81 (0.14), residues: 1364 loop : 0.07 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 553 HIS 0.003 0.001 HIS B 395 PHE 0.011 0.001 PHE A 549 TYR 0.017 0.001 TYR C 100 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 385 time to evaluate : 4.122 Fit side-chains REVERT: A 2 MET cc_start: 0.7403 (tpp) cc_final: 0.7113 (tpt) REVERT: A 241 GLU cc_start: 0.7741 (tt0) cc_final: 0.7523 (tt0) REVERT: A 438 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7510 (mt-10) REVERT: A 634 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8490 (tp40) REVERT: B 2 MET cc_start: 0.7404 (tpp) cc_final: 0.7116 (tpt) REVERT: B 128 ASN cc_start: 0.8358 (m110) cc_final: 0.8016 (t0) REVERT: B 438 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7510 (mt-10) REVERT: B 634 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8496 (tp40) REVERT: C 2 MET cc_start: 0.7406 (tpp) cc_final: 0.7117 (tpt) REVERT: C 438 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7514 (mt-10) REVERT: C 634 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8492 (tp40) REVERT: D 2 MET cc_start: 0.7402 (tpp) cc_final: 0.7114 (tpt) REVERT: D 128 ASN cc_start: 0.8358 (m110) cc_final: 0.8018 (t0) REVERT: D 438 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7510 (mt-10) REVERT: D 634 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8499 (tp40) outliers start: 37 outliers final: 21 residues processed: 409 average time/residue: 1.7816 time to fit residues: 857.6374 Evaluate side-chains 364 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 343 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 687 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 863 GLN A 905 ASN B 394 ASN B 687 GLN B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 863 GLN B 905 ASN C 394 ASN C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 905 ASN D 394 ASN ** D 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 GLN D 863 GLN D 905 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 33824 Z= 0.474 Angle : 0.645 10.975 46156 Z= 0.338 Chirality : 0.050 0.193 4844 Planarity : 0.004 0.037 6080 Dihedral : 6.220 58.072 4576 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.89 % Allowed : 7.99 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.47 (0.13), residues: 4076 helix: -0.42 (0.21), residues: 532 sheet: 0.96 (0.14), residues: 1372 loop : 0.19 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 553 HIS 0.007 0.001 HIS B 395 PHE 0.013 0.002 PHE A 989 TYR 0.025 0.002 TYR B 100 ARG 0.007 0.001 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 344 time to evaluate : 4.059 Fit side-chains REVERT: A 2 MET cc_start: 0.7169 (tpp) cc_final: 0.6934 (tpt) REVERT: B 2 MET cc_start: 0.7158 (tpp) cc_final: 0.6928 (tpt) REVERT: B 128 ASN cc_start: 0.8411 (m110) cc_final: 0.8100 (t0) REVERT: C 2 MET cc_start: 0.7172 (tpp) cc_final: 0.6938 (tpt) REVERT: D 2 MET cc_start: 0.7168 (tpp) cc_final: 0.6934 (tpt) REVERT: D 128 ASN cc_start: 0.8409 (m110) cc_final: 0.8100 (t0) outliers start: 31 outliers final: 20 residues processed: 369 average time/residue: 1.8766 time to fit residues: 811.8633 Evaluate side-chains 349 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 329 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 207 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 634 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 905 ASN B 634 GLN B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN B 905 ASN C 634 GLN C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 905 ASN D 634 GLN D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN D 905 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33824 Z= 0.290 Angle : 0.578 11.488 46156 Z= 0.301 Chirality : 0.046 0.174 4844 Planarity : 0.004 0.029 6080 Dihedral : 6.024 58.276 4576 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.17 % Allowed : 8.22 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 4076 helix: -0.22 (0.22), residues: 532 sheet: 0.99 (0.14), residues: 1372 loop : 0.19 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 553 HIS 0.005 0.001 HIS A 395 PHE 0.009 0.001 PHE C 549 TYR 0.022 0.002 TYR B 100 ARG 0.008 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 355 time to evaluate : 4.091 Fit side-chains REVERT: A 2 MET cc_start: 0.7170 (tpp) cc_final: 0.6941 (tpt) REVERT: B 2 MET cc_start: 0.7169 (tpp) cc_final: 0.6939 (tpt) REVERT: B 128 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8077 (t0) REVERT: C 2 MET cc_start: 0.7173 (tpp) cc_final: 0.6944 (tpt) REVERT: D 2 MET cc_start: 0.7167 (tpp) cc_final: 0.6936 (tpt) REVERT: D 128 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8075 (t0) outliers start: 41 outliers final: 22 residues processed: 383 average time/residue: 1.9075 time to fit residues: 856.5420 Evaluate side-chains 364 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 340 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 687 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN B 634 GLN B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 634 GLN C 687 GLN C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN D 634 GLN D 687 GLN D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33824 Z= 0.255 Angle : 0.561 11.334 46156 Z= 0.292 Chirality : 0.045 0.172 4844 Planarity : 0.004 0.028 6080 Dihedral : 5.909 58.010 4576 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.86 % Allowed : 8.88 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.57 (0.13), residues: 4076 helix: -0.15 (0.22), residues: 532 sheet: 1.05 (0.14), residues: 1352 loop : 0.18 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 553 HIS 0.004 0.001 HIS A 395 PHE 0.009 0.001 PHE D 225 TYR 0.021 0.001 TYR B 100 ARG 0.006 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 344 time to evaluate : 4.477 Fit side-chains REVERT: A 2 MET cc_start: 0.7151 (tpp) cc_final: 0.6939 (tpt) REVERT: A 241 GLU cc_start: 0.7756 (tt0) cc_final: 0.7536 (tt0) REVERT: B 2 MET cc_start: 0.7156 (tpp) cc_final: 0.6946 (tpt) REVERT: B 128 ASN cc_start: 0.8391 (m110) cc_final: 0.8063 (t0) REVERT: C 2 MET cc_start: 0.7153 (tpp) cc_final: 0.6942 (tpt) REVERT: D 2 MET cc_start: 0.7151 (tpp) cc_final: 0.6940 (tpt) REVERT: D 128 ASN cc_start: 0.8390 (m110) cc_final: 0.8062 (t0) outliers start: 30 outliers final: 22 residues processed: 368 average time/residue: 1.8764 time to fit residues: 811.8006 Evaluate side-chains 360 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 338 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 634 GLN A 739 HIS A 783 GLN A 863 GLN B 394 ASN B 634 GLN B 739 HIS B 783 GLN B 863 GLN C 394 ASN C 634 GLN C 739 HIS C 783 GLN C 863 GLN D 394 ASN D 634 GLN D 739 HIS D 783 GLN D 863 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33824 Z= 0.135 Angle : 0.499 10.629 46156 Z= 0.256 Chirality : 0.043 0.165 4844 Planarity : 0.003 0.038 6080 Dihedral : 5.427 59.043 4576 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.86 % Allowed : 9.25 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.60 (0.13), residues: 4076 helix: 0.12 (0.23), residues: 536 sheet: 1.11 (0.14), residues: 1336 loop : 0.11 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 553 HIS 0.003 0.001 HIS A 840 PHE 0.009 0.001 PHE B 225 TYR 0.016 0.001 TYR C 100 ARG 0.008 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 382 time to evaluate : 3.487 Fit side-chains REVERT: A 2 MET cc_start: 0.7157 (tpp) cc_final: 0.6932 (tpt) REVERT: A 241 GLU cc_start: 0.7731 (tt0) cc_final: 0.7485 (tt0) REVERT: A 438 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7439 (mt-10) REVERT: A 754 LYS cc_start: 0.8739 (mttp) cc_final: 0.8496 (mttm) REVERT: A 773 LYS cc_start: 0.8449 (mptp) cc_final: 0.8172 (mttp) REVERT: B 2 MET cc_start: 0.7158 (tpp) cc_final: 0.6936 (tpt) REVERT: B 128 ASN cc_start: 0.8353 (m110) cc_final: 0.7997 (t0) REVERT: B 438 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7439 (mt-10) REVERT: B 744 GLU cc_start: 0.7911 (pm20) cc_final: 0.7615 (pm20) REVERT: B 754 LYS cc_start: 0.8737 (mttp) cc_final: 0.8495 (mttm) REVERT: B 773 LYS cc_start: 0.8449 (mptp) cc_final: 0.8173 (mttp) REVERT: C 2 MET cc_start: 0.7159 (tpp) cc_final: 0.6935 (tpt) REVERT: C 314 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 438 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7440 (mt-10) REVERT: C 754 LYS cc_start: 0.8734 (mttp) cc_final: 0.8491 (mttm) REVERT: C 773 LYS cc_start: 0.8448 (mptp) cc_final: 0.8173 (mttp) REVERT: D 2 MET cc_start: 0.7157 (tpp) cc_final: 0.6934 (tpt) REVERT: D 128 ASN cc_start: 0.8350 (m110) cc_final: 0.7993 (t0) REVERT: D 438 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7439 (mt-10) REVERT: D 744 GLU cc_start: 0.7911 (pm20) cc_final: 0.7615 (pm20) REVERT: D 754 LYS cc_start: 0.8737 (mttp) cc_final: 0.8494 (mttm) REVERT: D 773 LYS cc_start: 0.8449 (mptp) cc_final: 0.8174 (mttp) outliers start: 30 outliers final: 20 residues processed: 406 average time/residue: 1.8329 time to fit residues: 875.5116 Evaluate side-chains 369 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 349 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 1.9990 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 0.8980 chunk 366 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 0.0570 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.8980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 634 GLN A 739 HIS A 817 GLN A 863 GLN A 896 ASN B 394 ASN B 634 GLN B 739 HIS B 817 GLN B 863 GLN B 896 ASN C 394 ASN C 634 GLN C 739 HIS C 863 GLN C 896 ASN D 394 ASN D 634 GLN D 739 HIS D 817 GLN D 863 GLN D 896 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33824 Z= 0.151 Angle : 0.510 10.669 46156 Z= 0.262 Chirality : 0.043 0.163 4844 Planarity : 0.003 0.034 6080 Dihedral : 5.391 57.610 4576 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.92 % Allowed : 9.54 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4076 helix: 0.25 (0.23), residues: 536 sheet: 1.22 (0.14), residues: 1316 loop : 0.10 (0.14), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 553 HIS 0.003 0.001 HIS D 395 PHE 0.013 0.001 PHE D 225 TYR 0.017 0.001 TYR D 100 ARG 0.008 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 363 time to evaluate : 4.175 Fit side-chains REVERT: A 2 MET cc_start: 0.7127 (tpp) cc_final: 0.6902 (tpt) REVERT: A 241 GLU cc_start: 0.7729 (tt0) cc_final: 0.7476 (tt0) REVERT: A 438 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7471 (mt-10) REVERT: A 655 MET cc_start: 0.7991 (mtt) cc_final: 0.7257 (mtt) REVERT: A 754 LYS cc_start: 0.8734 (mttp) cc_final: 0.8487 (mttm) REVERT: A 773 LYS cc_start: 0.8437 (mptp) cc_final: 0.8192 (mttp) REVERT: B 2 MET cc_start: 0.7125 (tpp) cc_final: 0.6903 (tpt) REVERT: B 128 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 438 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7474 (mt-10) REVERT: B 655 MET cc_start: 0.7994 (mtt) cc_final: 0.7260 (mtt) REVERT: B 754 LYS cc_start: 0.8730 (mttp) cc_final: 0.8482 (mttm) REVERT: B 773 LYS cc_start: 0.8438 (mptp) cc_final: 0.8192 (mttp) REVERT: C 2 MET cc_start: 0.7126 (tpp) cc_final: 0.6904 (tpt) REVERT: C 438 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7475 (mt-10) REVERT: C 655 MET cc_start: 0.7990 (mtt) cc_final: 0.7260 (mtt) REVERT: C 754 LYS cc_start: 0.8737 (mttp) cc_final: 0.8490 (mttm) REVERT: C 773 LYS cc_start: 0.8437 (mptp) cc_final: 0.8190 (mttp) REVERT: D 2 MET cc_start: 0.7127 (tpp) cc_final: 0.6904 (tpt) REVERT: D 128 ASN cc_start: 0.8357 (m110) cc_final: 0.8003 (t0) REVERT: D 438 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7473 (mt-10) REVERT: D 655 MET cc_start: 0.7997 (mtt) cc_final: 0.7266 (mtt) REVERT: D 754 LYS cc_start: 0.8732 (mttp) cc_final: 0.8484 (mttm) REVERT: D 773 LYS cc_start: 0.8437 (mptp) cc_final: 0.8191 (mttp) outliers start: 32 outliers final: 22 residues processed: 383 average time/residue: 1.9220 time to fit residues: 867.1813 Evaluate side-chains 370 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 347 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 0.0970 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 739 HIS A 817 GLN A 863 GLN B 634 GLN B 739 HIS B 817 GLN B 863 GLN C 634 GLN C 739 HIS C 863 GLN D 634 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33824 Z= 0.257 Angle : 0.561 10.004 46156 Z= 0.291 Chirality : 0.045 0.169 4844 Planarity : 0.004 0.038 6080 Dihedral : 5.779 56.989 4576 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.74 % Allowed : 9.77 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 4076 helix: 0.13 (0.23), residues: 532 sheet: 1.15 (0.14), residues: 1352 loop : 0.21 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 553 HIS 0.004 0.001 HIS B 395 PHE 0.013 0.001 PHE A 225 TYR 0.021 0.001 TYR D 100 ARG 0.008 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 360 time to evaluate : 4.130 Fit side-chains REVERT: A 241 GLU cc_start: 0.7743 (tt0) cc_final: 0.7498 (tt0) REVERT: A 655 MET cc_start: 0.7990 (mtt) cc_final: 0.7256 (mtt) REVERT: A 754 LYS cc_start: 0.8769 (mttp) cc_final: 0.8497 (mttm) REVERT: A 773 LYS cc_start: 0.8452 (mptp) cc_final: 0.8183 (mttp) REVERT: B 128 ASN cc_start: 0.8371 (m110) cc_final: 0.8053 (t0) REVERT: B 655 MET cc_start: 0.7991 (mtt) cc_final: 0.7257 (mtt) REVERT: B 754 LYS cc_start: 0.8767 (mttp) cc_final: 0.8496 (mttm) REVERT: B 773 LYS cc_start: 0.8450 (mptp) cc_final: 0.8184 (mttp) REVERT: C 438 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7473 (mt-10) REVERT: C 603 MET cc_start: 0.9011 (mtm) cc_final: 0.8804 (mtm) REVERT: C 655 MET cc_start: 0.7988 (mtt) cc_final: 0.7260 (mtt) REVERT: C 754 LYS cc_start: 0.8766 (mttp) cc_final: 0.8494 (mttm) REVERT: C 773 LYS cc_start: 0.8441 (mptp) cc_final: 0.8187 (mttp) REVERT: D 128 ASN cc_start: 0.8369 (m110) cc_final: 0.8052 (t0) REVERT: D 603 MET cc_start: 0.9019 (mtm) cc_final: 0.8808 (mtm) REVERT: D 655 MET cc_start: 0.7990 (mtt) cc_final: 0.7255 (mtt) REVERT: D 754 LYS cc_start: 0.8767 (mttp) cc_final: 0.8495 (mttm) REVERT: D 773 LYS cc_start: 0.8442 (mptp) cc_final: 0.8189 (mttp) outliers start: 26 outliers final: 22 residues processed: 380 average time/residue: 1.8729 time to fit residues: 835.1520 Evaluate side-chains 374 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 352 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 739 HIS A 817 GLN A 863 GLN B 634 GLN B 739 HIS B 817 GLN B 863 GLN C 634 GLN C 739 HIS C 863 GLN D 634 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069766 restraints weight = 47197.272| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.78 r_work: 0.2700 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33824 Z= 0.331 Angle : 0.597 10.657 46156 Z= 0.311 Chirality : 0.047 0.179 4844 Planarity : 0.004 0.040 6080 Dihedral : 6.025 59.268 4576 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.06 % Allowed : 9.51 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.72 (0.13), residues: 4076 helix: 0.23 (0.23), residues: 508 sheet: 1.14 (0.14), residues: 1372 loop : 0.20 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 553 HIS 0.005 0.001 HIS D 395 PHE 0.011 0.001 PHE C 225 TYR 0.024 0.002 TYR B 100 ARG 0.009 0.000 ARG D 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14589.85 seconds wall clock time: 258 minutes 9.58 seconds (15489.58 seconds total)