Starting phenix.real_space_refine on Thu Mar 21 00:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/03_2024/8hkm_34855_updated.pdb" } resolution = 2.95 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= 0.033 sd= 0.123 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: 7 Type Number sf(0) Gaussians K 11 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 212 5.16 5 C 18692 2.51 5 N 4784 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B GLU 949": "OE1" <-> "OE2" Residue "B PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1191": "OE1" <-> "OE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C GLU 715": "OE1" <-> "OE2" Residue "C TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 951": "OE1" <-> "OE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "C ASP 1194": "OD1" <-> "OD2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "D ASP 867": "OD1" <-> "OD2" Residue "D GLU 892": "OE1" <-> "OE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 28855 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 27 Unusual residues: {' K': 4, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' K': 2, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' K': 2, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 26 Unusual residues: {' K': 3, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4457 SG CYS A 777 97.513 66.786 13.845 1.00106.01 S ATOM 4463 SG CYS A 778 100.217 64.035 14.123 1.00106.62 S ATOM 4517 SG CYS A 785 96.837 63.244 12.492 1.00141.13 S ATOM 11645 SG CYS B 777 66.390 53.345 13.810 1.00100.38 S ATOM 11651 SG CYS B 778 63.502 50.638 14.045 1.00102.12 S ATOM 11705 SG CYS B 785 63.070 53.915 12.538 1.00120.59 S ATOM 18833 SG CYS C 777 52.812 84.392 13.755 1.00106.54 S ATOM 18839 SG CYS C 778 50.045 87.288 14.010 1.00109.23 S ATOM 18893 SG CYS C 785 53.220 87.802 12.382 1.00132.25 S ATOM 26021 SG CYS D 777 83.928 97.967 13.755 1.00 99.44 S ATOM 26027 SG CYS D 778 86.804 100.723 14.020 1.00104.05 S ATOM 26081 SG CYS D 785 87.249 97.422 12.372 1.00131.41 S Time building chain proxies: 15.42, per 1000 atoms: 0.53 Number of scatterers: 28855 At special positions: 0 Unit cell: (151.84, 151.84, 143.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 11 19.00 S 212 16.00 P 4 15.00 O 5148 8.00 N 4784 7.00 C 18692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 280 " distance=2.04 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 280 " distance=1.08 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 280 " distance=2.02 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: 11.17 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 778 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 777 " pdb=" ZN B1304 " pdb="ZN ZN B1304 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 778 " pdb=" ZN C1304 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1304 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 778 " pdb=" ZN D1305 " pdb="ZN ZN D1305 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1305 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1305 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1305 " - pdb=" SG CYS D 778 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 24 sheets defined 46.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 111 through 136 Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 174 through 197 Processing helix chain 'A' and resid 212 through 227 Proline residue: A 221 - end of helix removed outlier: 3.650A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.684A pdb=" N LEU A 244 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A 246 " --> pdb=" O TRP A 243 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 254 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 325 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.711A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 464 through 481 removed outlier: 3.516A pdb=" N VAL A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 548 through 558 removed outlier: 4.700A pdb=" N GLY A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.726A pdb=" N ARG A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.570A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 828 through 830 No H-bonds generated for 'chain 'A' and resid 828 through 830' Processing helix chain 'A' and resid 844 through 850 Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 894 through 911 removed outlier: 4.033A pdb=" N ASP A 898 " --> pdb=" O TYR A 895 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 902 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 911 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 929 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.717A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 4.123A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 962 through 966 Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.507A pdb=" N TYR A 980 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 981 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1022 through 1032 Processing helix chain 'A' and resid 1129 through 1142 removed outlier: 3.721A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'B' and resid 111 through 136 Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 174 through 197 Processing helix chain 'B' and resid 213 through 227 Proline residue: B 221 - end of helix removed outlier: 3.639A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 238 through 254 removed outlier: 3.767A pdb=" N LEU B 244 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 246 " --> pdb=" O TRP B 243 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 292 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 325 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.709A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 494 through 499 removed outlier: 4.554A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 548 through 558 removed outlier: 4.718A pdb=" N GLY B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.721A pdb=" N ARG B 643 " --> pdb=" O GLN B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 796 No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.570A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'B' and resid 866 through 872 Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 894 through 911 removed outlier: 4.020A pdb=" N ASP B 898 " --> pdb=" O TYR B 895 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS B 900 " --> pdb=" O ALA B 897 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 902 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 903 " --> pdb=" O LYS B 900 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 904 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 907 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 911 " --> pdb=" O MET B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 4.156A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.785A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.998A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 962 through 966 Processing helix chain 'B' and resid 972 through 983 removed outlier: 3.907A pdb=" N GLN B 981 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 996 Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1022 through 1032 Processing helix chain 'B' and resid 1129 through 1142 Processing helix chain 'B' and resid 1145 through 1160 Processing helix chain 'C' and resid 111 through 136 Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 174 through 197 Processing helix chain 'C' and resid 212 through 227 Proline residue: C 221 - end of helix removed outlier: 3.554A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.838A pdb=" N LEU C 244 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 246 " --> pdb=" O TRP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 292 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 325 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 383 through 395 removed outlier: 3.734A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 395 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 464 through 481 Processing helix chain 'C' and resid 494 through 499 removed outlier: 4.545A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.506A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 580 through 590 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.694A pdb=" N ARG C 643 " --> pdb=" O GLN C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 796 No H-bonds generated for 'chain 'C' and resid 793 through 796' Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.598A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 844 through 850 Processing helix chain 'C' and resid 866 through 872 Processing helix chain 'C' and resid 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' Processing helix chain 'C' and resid 894 through 911 removed outlier: 3.986A pdb=" N ASP C 898 " --> pdb=" O TYR C 895 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS C 900 " --> pdb=" O ALA C 897 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 902 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 903 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 904 " --> pdb=" O THR C 901 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 911 " --> pdb=" O MET C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.182A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.807A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 945 " --> pdb=" O ALA C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 3.964A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 962 through 965 No H-bonds generated for 'chain 'C' and resid 962 through 965' Processing helix chain 'C' and resid 972 through 983 removed outlier: 3.816A pdb=" N GLN C 981 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 996 Processing helix chain 'C' and resid 1014 through 1016 No H-bonds generated for 'chain 'C' and resid 1014 through 1016' Processing helix chain 'C' and resid 1022 through 1032 Processing helix chain 'C' and resid 1129 through 1142 removed outlier: 3.663A pdb=" N ARG C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1160 Processing helix chain 'D' and resid 111 through 136 Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 174 through 197 Processing helix chain 'D' and resid 213 through 227 removed outlier: 3.631A pdb=" N ILE D 217 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 3.565A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 239 through 254 removed outlier: 3.597A pdb=" N ASN D 254 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 292 Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 325 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.670A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 464 through 481 Processing helix chain 'D' and resid 494 through 499 removed outlier: 4.539A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 522 removed outlier: 3.525A pdb=" N ILE D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 533 Processing helix chain 'D' and resid 548 through 558 removed outlier: 4.712A pdb=" N GLY D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 575 No H-bonds generated for 'chain 'D' and resid 573 through 575' Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.696A pdb=" N ARG D 643 " --> pdb=" O GLN D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 812 through 822 removed outlier: 3.522A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 844 through 850 Processing helix chain 'D' and resid 866 through 872 Processing helix chain 'D' and resid 874 through 876 No H-bonds generated for 'chain 'D' and resid 874 through 876' Processing helix chain 'D' and resid 894 through 911 removed outlier: 3.987A pdb=" N ASP D 898 " --> pdb=" O TYR D 895 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS D 900 " --> pdb=" O ALA D 897 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 902 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 911 " --> pdb=" O MET D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 removed outlier: 4.179A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 951 removed outlier: 3.698A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.044A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 962 through 965 No H-bonds generated for 'chain 'D' and resid 962 through 965' Processing helix chain 'D' and resid 972 through 983 removed outlier: 3.574A pdb=" N TYR D 980 " --> pdb=" O THR D 977 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 981 " --> pdb=" O LEU D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 996 Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1022 through 1032 Processing helix chain 'D' and resid 1129 through 1142 removed outlier: 3.522A pdb=" N ARG D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1160 Processing sheet with id= A, first strand: chain 'A' and resid 505 through 508 removed outlier: 6.360A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 452 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 403 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A 376 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 405 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 378 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 407 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 750 through 753 Processing sheet with id= D, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.077A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 804 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 880 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER A 806 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 882 " --> pdb=" O SER A 806 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 916 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 882 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.846A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1039 through 1045 Processing sheet with id= G, first strand: chain 'B' and resid 505 through 508 removed outlier: 6.460A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 452 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR B 403 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 376 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 405 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL B 378 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 407 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.867A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 750 through 753 Processing sheet with id= J, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.094A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 804 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 880 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 806 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL B 882 " --> pdb=" O SER B 806 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.892A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1039 through 1045 Processing sheet with id= M, first strand: chain 'C' and resid 505 through 508 removed outlier: 6.465A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR C 403 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU C 376 " --> pdb=" O TYR C 403 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 405 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL C 378 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU C 407 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.894A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= P, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.111A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE C 804 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU C 880 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 806 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL C 882 " --> pdb=" O SER C 806 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER C 916 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 882 " --> pdb=" O SER C 916 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR C 918 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.711A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1039 through 1045 Processing sheet with id= S, first strand: chain 'D' and resid 505 through 508 removed outlier: 6.316A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR D 403 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU D 376 " --> pdb=" O TYR D 403 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 405 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL D 378 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU D 407 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.870A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 750 through 753 Processing sheet with id= V, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.060A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 804 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU D 880 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER D 806 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D 882 " --> pdb=" O SER D 806 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 916 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 882 " --> pdb=" O SER D 916 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 918 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.803A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1039 through 1045 1132 hydrogen bonds defined for protein. 2967 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: 9.88 Time building geometry restraints manager: 12.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9063 1.34 - 1.46: 6890 1.46 - 1.58: 13233 1.58 - 1.71: 10 1.71 - 1.83: 312 Bond restraints: 29508 Sorted by residual: bond pdb=" C PRO A 149 " pdb=" N LYS A 150 " ideal model delta sigma weight residual 1.330 1.382 -0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.72e+00 bond pdb=" CB CYS C 242 " pdb=" SG CYS C 242 " ideal model delta sigma weight residual 1.808 1.728 0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" C TRP D 228 " pdb=" N PRO D 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.18e-02 7.18e+03 5.43e+00 bond pdb=" CG PRO D 229 " pdb=" CD PRO D 229 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.19e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 76.57 - 89.48: 1 89.48 - 102.39: 125 102.39 - 115.30: 18666 115.30 - 128.21: 20993 128.21 - 141.12: 235 Bond angle restraints: 40020 Sorted by residual: angle pdb=" C PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta sigma weight residual 111.56 141.12 -29.56 1.65e+00 3.67e-01 3.21e+02 angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" C LYS D 150 " ideal model delta sigma weight residual 110.80 76.57 34.23 2.13e+00 2.20e-01 2.58e+02 angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" CB LYS D 150 " ideal model delta sigma weight residual 110.49 128.90 -18.41 1.69e+00 3.50e-01 1.19e+02 angle pdb=" N PRO C 149 " pdb=" CA PRO C 149 " pdb=" C PRO C 149 " ideal model delta sigma weight residual 112.47 127.57 -15.10 2.06e+00 2.36e-01 5.37e+01 angle pdb=" N PRO B 149 " pdb=" CA PRO B 149 " pdb=" C PRO B 149 " ideal model delta sigma weight residual 112.47 127.55 -15.08 2.06e+00 2.36e-01 5.36e+01 ... (remaining 40015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 16988 30.95 - 61.90: 667 61.90 - 92.85: 56 92.85 - 123.80: 8 123.80 - 154.75: 1 Dihedral angle restraints: 17720 sinusoidal: 7108 harmonic: 10612 Sorted by residual: dihedral pdb=" C PRO D 149 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual -120.70 -147.64 26.94 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" CB CYS D 242 " pdb=" SG CYS D 242 " pdb=" SG CYS D 280 " pdb=" CB CYS D 280 " ideal model delta sinusoidal sigma weight residual 93.00 -176.69 -90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 242 " pdb=" SG CYS B 242 " pdb=" SG CYS B 280 " pdb=" CB CYS B 280 " ideal model delta sinusoidal sigma weight residual 93.00 175.34 -82.34 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 17717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 4546 0.185 - 0.371: 3 0.371 - 0.556: 0 0.556 - 0.742: 2 0.742 - 0.927: 1 Chirality restraints: 4552 Sorted by residual: chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 1.79 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA PRO C 149 " pdb=" N PRO C 149 " pdb=" C PRO C 149 " pdb=" CB PRO C 149 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA PRO B 149 " pdb=" N PRO B 149 " pdb=" C PRO B 149 " pdb=" CB PRO B 149 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 4549 not shown) Planarity restraints: 5008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 149 " -0.054 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C PRO D 149 " 0.178 2.00e-02 2.50e+03 pdb=" O PRO D 149 " -0.065 2.00e-02 2.50e+03 pdb=" N LYS D 150 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 148 " -0.113 5.00e-02 4.00e+02 1.72e-01 4.75e+01 pdb=" N PRO A 149 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.102 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 148 " -0.111 5.00e-02 4.00e+02 1.70e-01 4.62e+01 pdb=" N PRO D 149 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.082 5.00e-02 4.00e+02 ... (remaining 5005 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.22: 22 2.22 - 2.95: 12644 2.95 - 3.68: 50516 3.68 - 4.41: 85029 4.41 - 5.14: 141043 Nonbonded interactions: 289254 Sorted by model distance: nonbonded pdb=" O CYS D 148 " pdb=" O PRO D 149 " model vdw 1.484 3.040 nonbonded pdb=" CZ ARG D 828 " pdb=" NZ LYS D 829 " model vdw 1.790 3.350 nonbonded pdb=" NH1 ARG D 828 " pdb=" NZ LYS D 829 " model vdw 1.817 3.200 nonbonded pdb=" NH1 ARG C 538 " pdb=" NE2 GLN C 540 " model vdw 1.839 3.200 nonbonded pdb=" NH2 ARG C 538 " pdb=" OE1 GLN C 540 " model vdw 1.944 2.520 ... (remaining 289249 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' and (resid 110 through 1205 or resid 1302)) selection = (chain 'B' and (resid 110 through 1205 or resid 1302)) selection = (chain 'C' and (resid 110 through 1205 or resid 1302)) selection = (chain 'D' and (resid 110 through 1205 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.270 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 81.140 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.170 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.003 0.101 29508 Z= 0.188 Angle : 0.714 34.234 40020 Z= 0.360 Chirality : 0.045 0.927 4552 Planarity : 0.006 0.172 5008 Dihedral : 16.007 154.747 10820 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 1.30 % Allowed : 19.11 % Favored : 79.59 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3532 helix: -0.35 (0.12), residues: 1664 sheet: -1.18 (0.29), residues: 324 loop : 0.05 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 204 HIS 0.011 0.001 HIS C 844 PHE 0.033 0.001 PHE B 275 TYR 0.021 0.001 TYR A 553 ARG 0.013 0.000 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 340 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 PRO cc_start: 0.8685 (Cg_endo) cc_final: 0.8402 (Cg_exo) REVERT: A 876 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8088 (p90) REVERT: B 174 MET cc_start: 0.7843 (ptp) cc_final: 0.7525 (pmm) REVERT: B 632 ASN cc_start: 0.8710 (m-40) cc_final: 0.8383 (m110) REVERT: B 844 HIS cc_start: 0.8120 (m170) cc_final: 0.7913 (m-70) REVERT: C 845 HIS cc_start: 0.8084 (t-90) cc_final: 0.7746 (t-90) REVERT: C 876 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7964 (p90) REVERT: C 1047 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7846 (t) REVERT: C 1138 LEU cc_start: 0.8858 (tp) cc_final: 0.8591 (tm) REVERT: D 192 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (mtm) REVERT: D 212 PHE cc_start: 0.8236 (t80) cc_final: 0.7938 (t80) REVERT: D 351 TYR cc_start: 0.7823 (t80) cc_final: 0.7615 (t80) outliers start: 41 outliers final: 33 residues processed: 374 average time/residue: 1.3549 time to fit residues: 593.8913 Evaluate side-chains 325 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 288 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.6980 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 0.5980 chunk 144 optimal weight: 0.4980 chunk 279 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 323 optimal weight: 9.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 218 ASN A 291 HIS A 427 GLN A 469 HIS A 470 GLN A 505 HIS A 535 HIS A 614 HIS A 871 GLN A 931 GLN A1174 GLN B 163 ASN B 470 GLN B 505 HIS B 535 HIS B 871 GLN B 879 ASN B 923 HIS B 931 GLN B1136 GLN C 291 HIS C 470 GLN C 505 HIS C 535 HIS C 543 GLN C 632 ASN ** C 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS D 427 GLN D 470 GLN D 505 HIS D 535 HIS D 543 GLN D 871 GLN D 931 GLN D1136 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 29508 Z= 0.253 Angle : 0.585 16.376 40020 Z= 0.289 Chirality : 0.042 0.281 4552 Planarity : 0.006 0.163 5008 Dihedral : 8.011 145.399 4028 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 3.54 % Allowed : 19.02 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.03 % 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: -0.02 (0.14), residues: 3532 helix: 0.31 (0.12), residues: 1636 sheet: -0.83 (0.26), residues: 360 loop : 0.04 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.008 0.001 HIS B 845 PHE 0.030 0.002 PHE B 275 TYR 0.022 0.001 TYR D 553 ARG 0.007 0.000 ARG D 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 316 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 139 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.8364 (Cg_exo) REVERT: A 279 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 289 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 329 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 566 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6430 (tpt) REVERT: A 876 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8154 (p90) REVERT: A 988 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8508 (tpt) REVERT: B 151 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: B 174 MET cc_start: 0.7829 (ptp) cc_final: 0.7584 (pmm) REVERT: B 192 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7668 (mpp) REVERT: B 212 PHE cc_start: 0.8599 (t80) cc_final: 0.7751 (t80) REVERT: C 845 HIS cc_start: 0.7893 (t-90) cc_final: 0.7586 (t-90) REVERT: C 876 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7996 (p90) REVERT: C 927 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7912 (mpp) REVERT: C 1047 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7831 (t) REVERT: D 212 PHE cc_start: 0.8051 (t80) cc_final: 0.7811 (t80) REVERT: D 630 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6745 (tp30) outliers start: 112 outliers final: 43 residues processed: 388 average time/residue: 1.3555 time to fit residues: 617.0814 Evaluate side-chains 355 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 323 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 chunk 288 optimal weight: 0.9990 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN C 490 GLN C 632 ASN C 844 HIS ** C 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 HIS ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D1136 GLN D1173 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 29508 Z= 0.298 Angle : 0.581 16.363 40020 Z= 0.283 Chirality : 0.043 0.255 4552 Planarity : 0.005 0.155 5008 Dihedral : 7.386 139.643 3997 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.58 % Allowed : 19.65 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.18 (0.14), residues: 3532 helix: 0.54 (0.13), residues: 1668 sheet: -0.95 (0.25), residues: 360 loop : 0.14 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 325 HIS 0.009 0.001 HIS C 844 PHE 0.014 0.001 PHE A 239 TYR 0.028 0.002 TYR B 553 ARG 0.006 0.000 ARG D 538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 319 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 139 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8388 (Cg_exo) REVERT: A 151 GLN cc_start: 0.7963 (mt0) cc_final: 0.7640 (mp10) REVERT: A 185 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8558 (pt) REVERT: A 275 PHE cc_start: 0.8117 (t80) cc_final: 0.7916 (t80) REVERT: A 279 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 289 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 566 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6387 (tpt) REVERT: A 876 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8146 (p90) REVERT: A 988 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8493 (tpt) REVERT: A 1140 LEU cc_start: 0.8171 (mp) cc_final: 0.7927 (tp) REVERT: B 174 MET cc_start: 0.7960 (ptp) cc_final: 0.7747 (pmm) REVERT: B 212 PHE cc_start: 0.8629 (t80) cc_final: 0.7558 (t80) REVERT: B 783 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7523 (tttp) REVERT: B 876 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8028 (p90) REVERT: B 935 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8466 (mtpp) REVERT: C 118 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7422 (t80) REVERT: C 174 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5905 (tpp) REVERT: C 289 ILE cc_start: 0.8930 (tp) cc_final: 0.8652 (tp) REVERT: C 566 MET cc_start: 0.7810 (tpt) cc_final: 0.7402 (tpt) REVERT: C 845 HIS cc_start: 0.7869 (t-90) cc_final: 0.7482 (t70) REVERT: C 876 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8021 (p90) REVERT: C 927 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.7839 (mpp) REVERT: C 1173 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.5578 (t70) REVERT: D 212 PHE cc_start: 0.8020 (t80) cc_final: 0.7706 (t80) REVERT: D 1138 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8249 (mm) outliers start: 113 outliers final: 52 residues processed: 388 average time/residue: 1.3614 time to fit residues: 623.4570 Evaluate side-chains 363 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 295 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 20.0000 chunk 243 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 325 optimal weight: 0.1980 chunk 344 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1136 GLN B1175 ASN C 632 ASN C 844 HIS C 845 HIS ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29508 Z= 0.174 Angle : 0.545 11.947 40020 Z= 0.266 Chirality : 0.041 0.258 4552 Planarity : 0.005 0.138 5008 Dihedral : 7.058 135.579 3991 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 2.97 % Allowed : 20.63 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.03 % 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: 0.40 (0.14), residues: 3532 helix: 0.74 (0.13), residues: 1668 sheet: -0.91 (0.25), residues: 360 loop : 0.23 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1132 HIS 0.008 0.001 HIS C 844 PHE 0.033 0.001 PHE B 275 TYR 0.029 0.001 TYR B 553 ARG 0.011 0.000 ARG D 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 319 time to evaluate : 3.321 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7926 (mmp80) REVERT: A 132 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 139 PRO cc_start: 0.8613 (Cg_endo) cc_final: 0.8371 (Cg_exo) REVERT: A 151 GLN cc_start: 0.8006 (mt0) cc_final: 0.7730 (mp10) REVERT: A 185 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8496 (pt) REVERT: A 275 PHE cc_start: 0.8110 (t80) cc_final: 0.7881 (t80) REVERT: A 279 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 289 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 566 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6411 (tpt) REVERT: A 876 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8147 (p90) REVERT: B 153 TYR cc_start: 0.8072 (m-80) cc_final: 0.7770 (m-80) REVERT: B 163 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8565 (p0) REVERT: B 212 PHE cc_start: 0.8254 (t80) cc_final: 0.7728 (t80) REVERT: B 876 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8034 (p90) REVERT: B 935 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8422 (mtpp) REVERT: C 168 LEU cc_start: 0.8844 (tm) cc_final: 0.8621 (tt) REVERT: C 174 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.6001 (tpp) REVERT: C 289 ILE cc_start: 0.8948 (tp) cc_final: 0.8666 (tp) REVERT: C 566 MET cc_start: 0.7754 (tpt) cc_final: 0.7241 (tpt) REVERT: C 845 HIS cc_start: 0.7767 (t70) cc_final: 0.7461 (t70) REVERT: C 876 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7959 (p90) REVERT: C 927 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7772 (mpp) REVERT: C 974 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7264 (ptp) REVERT: C 1047 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (t) REVERT: D 212 PHE cc_start: 0.7954 (t80) cc_final: 0.7574 (t80) REVERT: D 242 CYS cc_start: 0.6585 (t) cc_final: 0.6173 (t) REVERT: D 1138 LEU cc_start: 0.8393 (tm) cc_final: 0.8169 (mm) outliers start: 94 outliers final: 40 residues processed: 376 average time/residue: 1.3495 time to fit residues: 595.4348 Evaluate side-chains 363 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 309 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1142 ARG Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 chunk 141 optimal weight: 40.0000 chunk 293 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 HIS A1136 GLN B1136 GLN C 632 ASN C 844 HIS ** C 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 29508 Z= 0.556 Angle : 0.672 11.628 40020 Z= 0.329 Chirality : 0.048 0.264 4552 Planarity : 0.005 0.134 5008 Dihedral : 7.271 138.013 3989 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 4.24 % Allowed : 19.49 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.07 (0.14), residues: 3532 helix: 0.46 (0.12), residues: 1700 sheet: -1.23 (0.25), residues: 368 loop : 0.13 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 325 HIS 0.008 0.001 HIS C 844 PHE 0.015 0.002 PHE D 498 TYR 0.023 0.002 TYR B 553 ARG 0.009 0.001 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 328 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7686 (mtt90) REVERT: A 132 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8623 (p) REVERT: A 139 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: A 289 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8670 (tp) REVERT: A 555 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7539 (ttm-80) REVERT: A 566 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6499 (tpt) REVERT: A 876 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7963 (p90) REVERT: A 1139 SER cc_start: 0.8905 (t) cc_final: 0.8532 (p) REVERT: B 192 MET cc_start: 0.7681 (mpp) cc_final: 0.7427 (mpp) REVERT: B 212 PHE cc_start: 0.8483 (t80) cc_final: 0.8106 (t80) REVERT: B 783 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (tttp) REVERT: B 876 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8126 (p90) REVERT: B 1175 ASN cc_start: 0.8320 (m-40) cc_final: 0.8099 (t0) REVERT: C 174 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5860 (tpp) REVERT: C 216 MET cc_start: 0.8111 (mmm) cc_final: 0.7766 (mmm) REVERT: C 289 ILE cc_start: 0.8951 (tp) cc_final: 0.8664 (tp) REVERT: C 566 MET cc_start: 0.7831 (tpt) cc_final: 0.7341 (tpt) REVERT: C 845 HIS cc_start: 0.7865 (t70) cc_final: 0.7506 (t70) REVERT: C 876 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8057 (p90) REVERT: C 974 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7558 (ptp) REVERT: C 1157 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7827 (mtm) REVERT: C 1173 HIS cc_start: 0.5848 (OUTLIER) cc_final: 0.5564 (t70) REVERT: D 136 LEU cc_start: 0.8464 (mm) cc_final: 0.7997 (tt) REVERT: D 212 PHE cc_start: 0.8148 (t80) cc_final: 0.7846 (t80) REVERT: D 828 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7455 (tmt170) REVERT: D 1138 LEU cc_start: 0.8462 (tm) cc_final: 0.8252 (mm) outliers start: 134 outliers final: 68 residues processed: 410 average time/residue: 1.3172 time to fit residues: 637.1435 Evaluate side-chains 394 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 313 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1157 MET Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 1.9990 chunk 309 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 GLN C 844 HIS D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29508 Z= 0.184 Angle : 0.564 12.073 40020 Z= 0.274 Chirality : 0.041 0.267 4552 Planarity : 0.005 0.131 5008 Dihedral : 6.964 135.136 3989 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.31 % Rotamer: Outliers : 3.04 % Allowed : 21.39 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.46 (0.14), residues: 3532 helix: 0.76 (0.13), residues: 1672 sheet: -1.33 (0.26), residues: 324 loop : 0.38 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.008 0.001 HIS C 844 PHE 0.036 0.001 PHE B 275 TYR 0.027 0.001 TYR B 553 ARG 0.009 0.000 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 318 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7995 (mmp80) REVERT: A 132 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 139 PRO cc_start: 0.8617 (Cg_endo) cc_final: 0.8365 (Cg_exo) REVERT: A 185 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 289 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 876 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 1139 SER cc_start: 0.8916 (t) cc_final: 0.8587 (p) REVERT: B 212 PHE cc_start: 0.8619 (t80) cc_final: 0.8215 (t80) REVERT: B 783 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7556 (tttp) REVERT: B 935 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (mtpp) REVERT: B 988 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8548 (tpt) REVERT: C 174 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5883 (tpp) REVERT: C 216 MET cc_start: 0.8150 (mmm) cc_final: 0.7868 (mmm) REVERT: C 289 ILE cc_start: 0.8910 (tp) cc_final: 0.8630 (tp) REVERT: C 792 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7408 (p0) REVERT: C 845 HIS cc_start: 0.7792 (t70) cc_final: 0.7429 (t70) REVERT: C 876 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7919 (p90) REVERT: C 974 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7342 (ptp) REVERT: C 1173 HIS cc_start: 0.5794 (OUTLIER) cc_final: 0.5522 (t70) REVERT: D 212 PHE cc_start: 0.8022 (t80) cc_final: 0.7710 (t80) outliers start: 96 outliers final: 49 residues processed: 378 average time/residue: 1.3584 time to fit residues: 604.0840 Evaluate side-chains 362 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 301 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 343 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 HIS D1136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 29508 Z= 0.176 Angle : 0.549 12.716 40020 Z= 0.264 Chirality : 0.041 0.265 4552 Planarity : 0.005 0.131 5008 Dihedral : 6.671 133.343 3989 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 3.04 % Allowed : 21.68 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.58 (0.14), residues: 3532 helix: 0.92 (0.13), residues: 1672 sheet: -0.92 (0.26), residues: 364 loop : 0.33 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 243 HIS 0.006 0.001 HIS C 844 PHE 0.032 0.001 PHE B 283 TYR 0.026 0.001 TYR B 553 ARG 0.011 0.000 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 320 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7962 (mmp-170) REVERT: A 132 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8598 (p) REVERT: A 139 PRO cc_start: 0.8626 (Cg_endo) cc_final: 0.8343 (Cg_exo) REVERT: A 185 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 289 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 555 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7528 (ttm-80) REVERT: A 876 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8076 (p90) REVERT: A 1139 SER cc_start: 0.8921 (t) cc_final: 0.8591 (p) REVERT: B 129 LEU cc_start: 0.8888 (mt) cc_final: 0.8669 (tp) REVERT: B 153 TYR cc_start: 0.7925 (m-80) cc_final: 0.7653 (m-80) REVERT: B 212 PHE cc_start: 0.8243 (t80) cc_final: 0.7759 (t80) REVERT: B 216 MET cc_start: 0.7911 (pmm) cc_final: 0.7609 (pmm) REVERT: B 783 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7558 (tttp) REVERT: B 876 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8003 (p90) REVERT: B 935 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8392 (mtpp) REVERT: B 1175 ASN cc_start: 0.8258 (m-40) cc_final: 0.7948 (t0) REVERT: C 174 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5930 (tpp) REVERT: C 216 MET cc_start: 0.8139 (mmm) cc_final: 0.7870 (mmm) REVERT: C 351 TYR cc_start: 0.7660 (t80) cc_final: 0.7033 (t80) REVERT: C 845 HIS cc_start: 0.7754 (t70) cc_final: 0.7428 (t70) REVERT: C 876 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7967 (p90) REVERT: C 974 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7243 (ptp) REVERT: C 1047 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7849 (t) REVERT: C 1173 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5540 (t70) REVERT: D 828 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7415 (tmt170) outliers start: 96 outliers final: 43 residues processed: 375 average time/residue: 1.3365 time to fit residues: 593.4765 Evaluate side-chains 362 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 305 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.9990 chunk 137 optimal weight: 0.0980 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 233 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 816 ASN A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 GLN C 844 HIS D1136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 29508 Z= 0.192 Angle : 0.569 11.447 40020 Z= 0.276 Chirality : 0.041 0.271 4552 Planarity : 0.005 0.132 5008 Dihedral : 6.652 132.656 3989 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 2.88 % Allowed : 22.28 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3532 helix: 0.91 (0.13), residues: 1696 sheet: -0.82 (0.26), residues: 364 loop : 0.36 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1132 HIS 0.006 0.001 HIS C 844 PHE 0.038 0.001 PHE A 275 TYR 0.023 0.001 TYR D 582 ARG 0.012 0.000 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 309 time to evaluate : 3.382 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8563 (tp) cc_final: 0.8346 (tt) REVERT: A 132 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 139 PRO cc_start: 0.8638 (Cg_endo) cc_final: 0.8346 (Cg_exo) REVERT: A 185 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 216 MET cc_start: 0.8311 (mmm) cc_final: 0.7767 (mmt) REVERT: A 289 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8628 (tp) REVERT: A 355 GLU cc_start: 0.8355 (tt0) cc_final: 0.8126 (tt0) REVERT: A 555 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7531 (ttm-80) REVERT: A 876 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8152 (p90) REVERT: A 1139 SER cc_start: 0.8919 (t) cc_final: 0.8592 (p) REVERT: B 128 LEU cc_start: 0.8295 (tp) cc_final: 0.7842 (mp) REVERT: B 129 LEU cc_start: 0.8883 (mt) cc_final: 0.8653 (tp) REVERT: B 212 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7894 (t80) REVERT: B 217 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 876 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8128 (p90) REVERT: B 935 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: B 1174 GLN cc_start: 0.6378 (mm110) cc_final: 0.5349 (mt0) REVERT: C 174 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5924 (tpp) REVERT: C 289 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8670 (tp) REVERT: C 845 HIS cc_start: 0.7739 (t70) cc_final: 0.7418 (t70) REVERT: C 876 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7965 (p90) REVERT: C 927 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7913 (mpp) REVERT: C 974 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7237 (ptp) REVERT: C 1047 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7847 (t) REVERT: C 1173 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5558 (t70) REVERT: D 212 PHE cc_start: 0.8050 (t80) cc_final: 0.7737 (t80) REVERT: D 828 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7416 (tmt170) outliers start: 91 outliers final: 40 residues processed: 366 average time/residue: 1.3602 time to fit residues: 585.1435 Evaluate side-chains 358 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 301 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 5.9990 chunk 328 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 30.0000 chunk 192 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 288 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 GLN C 844 HIS D 218 ASN D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 29508 Z= 0.183 Angle : 0.572 12.749 40020 Z= 0.277 Chirality : 0.041 0.266 4552 Planarity : 0.005 0.134 5008 Dihedral : 6.522 131.461 3989 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.45 % Rotamer: Outliers : 2.25 % Allowed : 23.10 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3532 helix: 0.94 (0.13), residues: 1696 sheet: -0.74 (0.26), residues: 364 loop : 0.37 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 243 HIS 0.006 0.001 HIS C 844 PHE 0.033 0.001 PHE B 283 TYR 0.022 0.001 TYR D 582 ARG 0.011 0.000 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 306 time to evaluate : 3.485 Fit side-chains revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 139 PRO cc_start: 0.8632 (Cg_endo) cc_final: 0.8334 (Cg_exo) REVERT: A 185 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8534 (pt) REVERT: A 216 MET cc_start: 0.8334 (mmm) cc_final: 0.7771 (mmt) REVERT: A 289 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 355 GLU cc_start: 0.8308 (tt0) cc_final: 0.7892 (tt0) REVERT: A 555 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7461 (ttm-80) REVERT: A 876 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8155 (p90) REVERT: A 1139 SER cc_start: 0.8878 (t) cc_final: 0.8526 (p) REVERT: B 128 LEU cc_start: 0.8310 (tp) cc_final: 0.7853 (mp) REVERT: B 129 LEU cc_start: 0.8900 (mt) cc_final: 0.8652 (tp) REVERT: B 217 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8612 (tp) REVERT: B 848 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: B 876 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8073 (p90) REVERT: B 935 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8372 (mtpp) REVERT: C 174 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5948 (tpp) REVERT: C 216 MET cc_start: 0.8268 (mmm) cc_final: 0.7913 (mmm) REVERT: C 289 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8643 (tp) REVERT: C 792 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7553 (p0) REVERT: C 845 HIS cc_start: 0.7724 (t70) cc_final: 0.7408 (t70) REVERT: C 876 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7975 (p90) REVERT: C 974 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7227 (ptp) REVERT: C 1020 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7811 (pmm-80) REVERT: C 1047 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7834 (t) REVERT: C 1173 HIS cc_start: 0.5813 (OUTLIER) cc_final: 0.5574 (t70) REVERT: D 124 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7775 (pt) REVERT: D 212 PHE cc_start: 0.8221 (t80) cc_final: 0.7924 (t80) REVERT: D 828 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7413 (tmt170) outliers start: 71 outliers final: 40 residues processed: 350 average time/residue: 1.3976 time to fit residues: 573.0680 Evaluate side-chains 349 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 291 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 354 optimal weight: 0.8980 chunk 326 optimal weight: 0.0370 chunk 282 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN B1136 GLN C 844 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 29508 Z= 0.196 Angle : 0.588 13.976 40020 Z= 0.284 Chirality : 0.042 0.314 4552 Planarity : 0.005 0.136 5008 Dihedral : 6.452 130.719 3989 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 2.03 % Allowed : 23.48 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3532 helix: 0.97 (0.13), residues: 1696 sheet: -0.68 (0.26), residues: 364 loop : 0.37 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 243 HIS 0.006 0.001 HIS C 844 PHE 0.040 0.001 PHE A 275 TYR 0.023 0.001 TYR D 582 ARG 0.012 0.000 ARG C 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 3.543 Fit side-chains revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 139 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8327 (Cg_exo) REVERT: A 185 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8537 (pt) REVERT: A 216 MET cc_start: 0.8386 (mmm) cc_final: 0.7804 (mmt) REVERT: A 235 PHE cc_start: 0.8691 (t80) cc_final: 0.8478 (t80) REVERT: A 289 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8581 (tp) REVERT: A 355 GLU cc_start: 0.8279 (tt0) cc_final: 0.7849 (tt0) REVERT: A 555 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7452 (ttm-80) REVERT: A 876 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8154 (p90) REVERT: A 1139 SER cc_start: 0.8901 (t) cc_final: 0.8504 (p) REVERT: B 128 LEU cc_start: 0.8316 (tp) cc_final: 0.7855 (mp) REVERT: B 129 LEU cc_start: 0.8900 (mt) cc_final: 0.8657 (tp) REVERT: B 848 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: B 876 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.8111 (p90) REVERT: B 935 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (mtpp) REVERT: B 988 MET cc_start: 0.8761 (tpt) cc_final: 0.8527 (mmt) REVERT: B 1174 GLN cc_start: 0.6360 (mm110) cc_final: 0.5343 (mt0) REVERT: C 114 ARG cc_start: 0.6248 (tpp-160) cc_final: 0.5642 (mtp-110) REVERT: C 174 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5949 (tpp) REVERT: C 216 MET cc_start: 0.8275 (mmm) cc_final: 0.7921 (mmm) REVERT: C 289 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 792 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7565 (p0) REVERT: C 845 HIS cc_start: 0.7715 (t70) cc_final: 0.7408 (t70) REVERT: C 876 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7982 (p90) REVERT: C 974 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7220 (ptp) REVERT: C 1047 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7829 (t) REVERT: C 1173 HIS cc_start: 0.5817 (OUTLIER) cc_final: 0.5584 (t70) REVERT: D 124 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7758 (pt) REVERT: D 212 PHE cc_start: 0.8172 (t80) cc_final: 0.7877 (t80) REVERT: D 447 MET cc_start: 0.8366 (tpp) cc_final: 0.8078 (mmm) REVERT: D 828 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (tmt170) outliers start: 64 outliers final: 37 residues processed: 340 average time/residue: 1.3792 time to fit residues: 548.7360 Evaluate side-chains 346 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 292 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1201 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 GLN C 844 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.104018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081909 restraints weight = 65159.143| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.63 r_work: 0.3110 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29508 Z= 0.245 Angle : 0.599 14.040 40020 Z= 0.291 Chirality : 0.042 0.275 4552 Planarity : 0.005 0.138 5008 Dihedral : 6.407 130.895 3989 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 2.22 % Allowed : 23.45 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.66 (0.15), residues: 3532 helix: 0.93 (0.13), residues: 1696 sheet: -0.70 (0.26), residues: 364 loop : 0.37 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 243 HIS 0.008 0.001 HIS B 787 PHE 0.036 0.001 PHE B 283 TYR 0.022 0.001 TYR D 582 ARG 0.012 0.000 ARG C 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9587.88 seconds wall clock time: 170 minutes 55.37 seconds (10255.37 seconds total)