Starting phenix.real_space_refine on Mon Nov 20 03:45:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/11_2023/8hkm_34855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/11_2023/8hkm_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_34855/11_2023/8hkm_34855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/11_2023/8hkm_34855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/11_2023/8hkm_34855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkm_34855/11_2023/8hkm_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 24 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: 24 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: 24 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: 24 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: 15.04, per 1000 atoms: 0.52 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: 11.37 Conformation dependent library (CDL) restraints added in 4.8 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: 7.16 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: 10.92 Time building geometry restraints manager: 12.09 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 - 18.06: 15749 18.06 - 36.13: 1435 36.13 - 54.19: 391 54.19 - 72.25: 85 72.25 - 90.31: 32 Dihedral angle restraints: 17692 sinusoidal: 7080 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 17689 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.360 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 81.020 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.700 ------------------------------------------------------------------------------- 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 : 15.554 89.858 10792 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 *********************** 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 : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 374 average time/residue: 1.3813 time to fit residues: 606.9293 Evaluate side-chains 322 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 289 time to evaluate : 3.664 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 3 average time/residue: 0.5640 time to fit residues: 7.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 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: 1.6982 ------------------------------------------------------------------------------- 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 490 GLN C 505 HIS C 535 HIS 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 291 HIS 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 29508 Z= 0.244 Angle : 0.584 16.382 40020 Z= 0.288 Chirality : 0.042 0.272 4552 Planarity : 0.006 0.161 5008 Dihedral : 5.364 75.549 3948 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 4.05 % Allowed : 18.96 % Favored : 76.99 % 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: -0.03 (0.14), residues: 3532 helix: 0.30 (0.12), residues: 1636 sheet: -0.84 (0.26), residues: 360 loop : 0.05 (0.17), residues: 1536 *********************** 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 448 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 320 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 57 residues processed: 406 average time/residue: 1.3614 time to fit residues: 652.3569 Evaluate side-chains 361 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 304 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 41 residues processed: 17 average time/residue: 0.6451 time to fit residues: 19.3302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 220 optimal weight: 0.1980 chunk 89 optimal weight: 30.0000 chunk 323 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 923 HIS A1136 GLN B1136 GLN C 543 GLN C 632 ASN C 844 HIS ** C 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 HIS D1136 GLN D1173 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 29508 Z= 0.385 Angle : 0.614 15.117 40020 Z= 0.299 Chirality : 0.044 0.330 4552 Planarity : 0.005 0.154 5008 Dihedral : 5.409 77.311 3948 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 4.18 % Allowed : 19.37 % Favored : 76.46 % 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: 0.11 (0.14), residues: 3532 helix: 0.49 (0.13), residues: 1672 sheet: -1.09 (0.25), residues: 364 loop : 0.11 (0.17), residues: 1496 *********************** 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 450 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 318 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 75 residues processed: 405 average time/residue: 1.3474 time to fit residues: 645.1752 Evaluate side-chains 373 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 298 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 53 residues processed: 22 average time/residue: 0.8835 time to fit residues: 29.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 168 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 344 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29508 Z= 0.185 Angle : 0.557 11.674 40020 Z= 0.271 Chirality : 0.041 0.265 4552 Planarity : 0.005 0.138 5008 Dihedral : 5.227 75.846 3948 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.31 % Rotamer: Outliers : 3.39 % Allowed : 20.28 % Favored : 76.33 % 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: 0.35 (0.14), residues: 3532 helix: 0.70 (0.13), residues: 1668 sheet: -1.00 (0.25), residues: 360 loop : 0.21 (0.17), residues: 1504 *********************** 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 421 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 314 time to evaluate : 3.180 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 57 residues processed: 388 average time/residue: 1.3334 time to fit residues: 614.7748 Evaluate side-chains 354 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 297 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 45 residues processed: 12 average time/residue: 0.7083 time to fit residues: 16.3137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 4 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 0.5980 chunk 308 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- 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 A1136 GLN B1136 GLN C 632 ASN C 844 HIS C 845 HIS ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 29508 Z= 0.527 Angle : 0.665 11.798 40020 Z= 0.325 Chirality : 0.047 0.262 4552 Planarity : 0.005 0.135 5008 Dihedral : 5.516 78.747 3948 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 4.30 % Allowed : 20.06 % Favored : 75.63 % 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: 0.09 (0.14), residues: 3532 helix: 0.49 (0.13), residues: 1696 sheet: -1.23 (0.25), residues: 364 loop : 0.11 (0.17), residues: 1472 *********************** 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 456 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 320 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 75 residues processed: 414 average time/residue: 1.3146 time to fit residues: 645.4349 Evaluate side-chains 378 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 303 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 57 residues processed: 18 average time/residue: 0.8934 time to fit residues: 24.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** B1175 ASN C 844 HIS C1174 GLN D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 29508 Z= 0.251 Angle : 0.583 12.210 40020 Z= 0.283 Chirality : 0.042 0.261 4552 Planarity : 0.005 0.133 5008 Dihedral : 5.341 78.150 3948 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 3.39 % Allowed : 21.55 % Favored : 75.06 % 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: 0.35 (0.14), residues: 3532 helix: 0.67 (0.13), residues: 1696 sheet: -1.44 (0.26), residues: 324 loop : 0.34 (0.17), residues: 1512 *********************** 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 416 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 309 time to evaluate : 3.507 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 72 residues processed: 391 average time/residue: 1.3506 time to fit residues: 627.0812 Evaluate side-chains 374 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 302 time to evaluate : 3.556 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 60 residues processed: 12 average time/residue: 0.6589 time to fit residues: 15.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 289 optimal weight: 0.9990 chunk 192 optimal weight: 0.0870 chunk 343 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.1958 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= 0.180 Angle : 0.549 12.379 40020 Z= 0.266 Chirality : 0.041 0.262 4552 Planarity : 0.005 0.133 5008 Dihedral : 5.042 78.101 3948 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.54 % Allowed : 21.52 % Favored : 74.94 % 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: 0.53 (0.15), residues: 3532 helix: 0.88 (0.13), residues: 1688 sheet: -1.03 (0.25), residues: 364 loop : 0.29 (0.17), residues: 1480 *********************** 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 431 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 319 time to evaluate : 3.742 Fit side-chains revert: symmetry clash outliers start: 112 outliers final: 70 residues processed: 397 average time/residue: 1.3474 time to fit residues: 638.2528 Evaluate side-chains 365 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 295 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 58 residues processed: 13 average time/residue: 0.6550 time to fit residues: 16.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 B1175 ASN C 844 HIS D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29508 Z= 0.272 Angle : 0.597 13.301 40020 Z= 0.289 Chirality : 0.043 0.276 4552 Planarity : 0.005 0.135 5008 Dihedral : 5.085 79.188 3948 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 3.23 % Allowed : 22.34 % Favored : 74.43 % 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: 0.51 (0.14), residues: 3532 helix: 0.86 (0.13), residues: 1692 sheet: -1.00 (0.25), residues: 364 loop : 0.28 (0.17), residues: 1476 *********************** 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 408 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 306 time to evaluate : 3.455 Fit side-chains revert: symmetry clash outliers start: 102 outliers final: 68 residues processed: 382 average time/residue: 1.3596 time to fit residues: 618.2523 Evaluate side-chains 362 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 58 residues processed: 11 average time/residue: 0.6443 time to fit residues: 15.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 319 optimal weight: 40.0000 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 98 optimal weight: 0.0470 chunk 288 optimal weight: 0.9980 chunk 302 optimal weight: 0.3980 chunk 318 optimal weight: 5.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29508 Z= 0.200 Angle : 0.593 12.767 40020 Z= 0.288 Chirality : 0.042 0.310 4552 Planarity : 0.005 0.137 5008 Dihedral : 5.035 79.012 3948 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 2.59 % Allowed : 22.78 % Favored : 74.62 % 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: 0.58 (0.15), residues: 3532 helix: 0.92 (0.13), residues: 1688 sheet: -0.85 (0.26), residues: 360 loop : 0.29 (0.17), residues: 1484 *********************** 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 387 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 305 time to evaluate : 3.798 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 63 residues processed: 368 average time/residue: 1.3743 time to fit residues: 600.2718 Evaluate side-chains 355 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 292 time to evaluate : 3.552 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 55 residues processed: 8 average time/residue: 0.6770 time to fit residues: 12.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 206 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 326 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29508 Z= 0.181 Angle : 0.586 13.995 40020 Z= 0.283 Chirality : 0.041 0.303 4552 Planarity : 0.005 0.138 5008 Dihedral : 4.917 78.363 3948 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 2.18 % Allowed : 23.45 % Favored : 74.37 % 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: 1.00 (0.13), residues: 1688 sheet: -0.80 (0.26), residues: 364 loop : 0.32 (0.17), residues: 1480 ********************** 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 370 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 301 time to evaluate : 3.536 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 60 residues processed: 361 average time/residue: 1.3421 time to fit residues: 574.0330 Evaluate side-chains 348 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 3.549 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 57 residues processed: 4 average time/residue: 0.8854 time to fit residues: 9.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.0070 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081877 restraints weight = 64980.901| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.62 r_work: 0.3107 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 29508 Z= 0.257 Angle : 0.615 13.722 40020 Z= 0.297 Chirality : 0.043 0.270 4552 Planarity : 0.005 0.140 5008 Dihedral : 4.968 78.613 3948 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 2.41 % Allowed : 23.42 % Favored : 74.18 % 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: 0.53 (0.14), residues: 3532 helix: 0.88 (0.13), residues: 1716 sheet: -0.78 (0.26), residues: 364 loop : 0.21 (0.17), residues: 1452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9854.93 seconds wall clock time: 176 minutes 42.75 seconds (10602.75 seconds total)