Starting phenix.real_space_refine on Fri Aug 9 10:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e74_27935/08_2024/8e74_27935.cif" } resolution = 2.94 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= 0.003 sd= 0.170 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 Zn 2 6.06 5 P 106 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 15861 2.51 5 N 4565 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z GLU 41": "OE1" <-> "OE2" Residue "Z TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 83": "OE1" <-> "OE2" Residue "Z GLU 87": "OE1" <-> "OE2" Residue "Z GLU 88": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C GLU 645": "OE1" <-> "OE2" Residue "C GLU 646": "OE1" <-> "OE2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "C TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 694": "OD1" <-> "OD2" Residue "C GLU 697": "OE1" <-> "OE2" Residue "C ASP 758": "OD1" <-> "OD2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 909": "OD1" <-> "OD2" Residue "C GLU 965": "OE1" <-> "OE2" Residue "C ASP 1003": "OD1" <-> "OD2" Residue "C TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1094": "OD1" <-> "OD2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 608": "OE1" <-> "OE2" Residue "D GLU 645": "OE1" <-> "OE2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 735": "OD1" <-> "OD2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D GLU 784": "OE1" <-> "OE2" Residue "D PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 879": "OD1" <-> "OD2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D GLU 894": "OE1" <-> "OE2" Residue "D TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D GLU 1140": "OE1" <-> "OE2" Residue "D TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1185": "OE1" <-> "OE2" Residue "D GLU 1228": "OE1" <-> "OE2" Residue "D GLU 1277": "OE1" <-> "OE2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25815 Number of models: 1 Model: "" Number of chains: 10 Chain: "Z" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8600 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1047} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9920 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "O" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 751 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 678 Classifications: {'RNA': 32} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 29} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13556 SG CYS D 60 21.001 35.712 111.958 1.00 80.49 S ATOM 13574 SG CYS D 62 20.954 34.463 115.063 1.00 85.19 S ATOM 13683 SG CYS D 75 18.042 36.677 115.004 1.00 85.24 S ATOM 13709 SG CYS D 78 21.654 37.288 115.288 1.00 78.29 S ATOM 20124 SG CYS D 891 36.009 98.501 87.474 1.00 52.24 S ATOM 20691 SG CYS D 968 38.045 95.031 88.631 1.00 47.29 S ATOM 20733 SG CYS D 975 36.802 95.312 85.263 1.00 56.83 S ATOM 20751 SG CYS D 978 38.977 97.414 85.723 1.00 44.58 S Time building chain proxies: 14.33, per 1000 atoms: 0.56 Number of scatterers: 25815 At special positions: 0 Unit cell: (125.57, 128.817, 199.18, 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 2 29.99 S 88 16.00 P 106 15.00 Mg 1 11.99 O 5192 8.00 N 4565 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 42 sheets defined 39.7% alpha, 17.7% beta 43 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 9.72 Creating SS restraints... Processing helix chain 'Z' and resid 33 through 45 removed outlier: 3.850A pdb=" N SER Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS Z 45 " --> pdb=" O GLU Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 73 removed outlier: 4.044A pdb=" N GLN Z 71 " --> pdb=" O GLU Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 116 through 125 removed outlier: 3.848A pdb=" N ALA Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 151 Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.541A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.176A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.061A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.515A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.845A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.967A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.679A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.606A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.645A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.699A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.633A pdb=" N ILE C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.618A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.685A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.062A pdb=" N ALA C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.852A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.525A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.592A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.826A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.963A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 removed outlier: 3.535A pdb=" N ILE C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.749A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.506A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.613A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.290A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.954A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.750A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 187 removed outlier: 3.618A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.644A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.622A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.660A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.987A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.614A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.919A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.582A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.530A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.554A pdb=" N ARG D 459 " --> pdb=" O PHE D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.254A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.583A pdb=" N ALA D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.594A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.606A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.754A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.167A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.541A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.526A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.696A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.525A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.325A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.878A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.751A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.549A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'Z' and resid 79 through 83 removed outlier: 3.533A pdb=" N GLN Z 81 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL Z 51 " --> pdb=" O PHE Z 132 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE Z 132 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS Z 53 " --> pdb=" O THR Z 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 86 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 12 removed outlier: 5.844A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.601A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.635A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.330A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.540A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.451A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.071A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.294A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.455A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 215 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.179A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.548A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.414A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.667A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.703A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.724A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.518A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 784 through 785 removed outlier: 5.162A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.818A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD5, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD6, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.747A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.597A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.513A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 328 through 330 removed outlier: 3.659A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.391A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.956A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 6.262A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.785A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 1003 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 13.89 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7632 1.33 - 1.45: 3931 1.45 - 1.57: 14552 1.57 - 1.69: 208 1.69 - 1.81: 155 Bond restraints: 26478 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" CB ASP C 903 " pdb=" CG ASP C 903 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.38e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CA GLY C 608 " pdb=" C GLY C 608 " ideal model delta sigma weight residual 1.516 1.500 0.016 1.12e-02 7.97e+03 2.06e+00 ... (remaining 26473 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 1156 105.93 - 112.95: 14470 112.95 - 119.98: 9209 119.98 - 127.00: 10996 127.00 - 134.03: 517 Bond angle restraints: 36348 Sorted by residual: angle pdb=" C PRO B 28 " pdb=" N GLY B 29 " pdb=" CA GLY B 29 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" N ILE B 159 " pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N VAL C 780 " pdb=" CA VAL C 780 " pdb=" C VAL C 780 " ideal model delta sigma weight residual 111.91 109.01 2.90 8.90e-01 1.26e+00 1.06e+01 angle pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 113.12 109.05 4.07 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N GLY D 508 " pdb=" CA GLY D 508 " pdb=" C GLY D 508 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.28e+00 ... (remaining 36343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 15294 34.30 - 68.59: 692 68.59 - 102.89: 38 102.89 - 137.19: 0 137.19 - 171.48: 5 Dihedral angle restraints: 16029 sinusoidal: 7309 harmonic: 8720 Sorted by residual: dihedral pdb=" CA ARG C 563 " pdb=" C ARG C 563 " pdb=" N LYS C 564 " pdb=" CA LYS C 564 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ALA C 766 " pdb=" C ALA C 766 " pdb=" N GLU C 767 " pdb=" CA GLU C 767 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DA P 118 " pdb=" C3' DA P 118 " pdb=" O3' DA P 118 " pdb=" P DA P 119 " ideal model delta sinusoidal sigma weight residual 220.00 48.52 171.48 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2710 0.034 - 0.069: 1011 0.069 - 0.103: 297 0.103 - 0.137: 147 0.137 - 0.172: 7 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE C1112 " pdb=" N ILE C1112 " pdb=" C ILE C1112 " pdb=" CB ILE C1112 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE D1149 " pdb=" N ILE D1149 " pdb=" C ILE D1149 " pdb=" CB ILE D1149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 4169 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 144 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C ARG D 144 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG D 144 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS D 145 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D 434 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO D 658 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " -0.024 5.00e-02 4.00e+02 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 30 2.31 - 2.96: 11987 2.96 - 3.61: 35937 3.61 - 4.25: 59233 4.25 - 4.90: 100247 Nonbonded interactions: 207434 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.665 2.170 nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 1.873 2.170 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 2.005 3.040 nonbonded pdb=" O ASP C 761 " pdb=" OG1 THR C 762 " model vdw 2.030 3.040 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.049 2.170 ... (remaining 207429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } 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: 1.120 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: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 84.580 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.004 0.052 26478 Z= 0.289 Angle : 0.645 7.312 36348 Z= 0.387 Chirality : 0.043 0.172 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.975 171.483 10425 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 2.63 % Allowed : 9.89 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3032 helix: 0.19 (0.16), residues: 1107 sheet: -0.81 (0.26), residues: 416 loop : -1.44 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.005 0.001 HIS C 372 PHE 0.013 0.001 PHE C 906 TYR 0.016 0.001 TYR A 168 ARG 0.007 0.001 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 125 ASN cc_start: 0.8532 (m-40) cc_final: 0.8288 (m-40) REVERT: A 137 GLU cc_start: 0.7885 (pp20) cc_final: 0.7664 (pp20) REVERT: B 177 LYS cc_start: 0.8144 (mttp) cc_final: 0.7801 (tttp) REVERT: C 336 GLU cc_start: 0.6677 (tp30) cc_final: 0.6427 (tp30) REVERT: C 393 MET cc_start: 0.8583 (mmt) cc_final: 0.8150 (mmt) REVERT: C 429 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6649 (tp30) REVERT: C 440 MET cc_start: 0.9028 (ttt) cc_final: 0.8612 (ttt) REVERT: C 529 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 733 ASP cc_start: 0.8435 (m-30) cc_final: 0.8139 (m-30) REVERT: C 758 ASP cc_start: 0.8160 (p0) cc_final: 0.7821 (p0) REVERT: C 760 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7362 (mtt90) REVERT: C 814 LEU cc_start: 0.1939 (OUTLIER) cc_final: 0.1247 (mm) REVERT: C 903 ASP cc_start: 0.8538 (p0) cc_final: 0.8333 (p0) REVERT: C 947 ASP cc_start: 0.7765 (p0) cc_final: 0.7315 (p0) REVERT: D 123 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8043 (mptp) REVERT: D 177 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.3691 (mp) REVERT: D 530 GLU cc_start: 0.7613 (tt0) cc_final: 0.7215 (pm20) REVERT: D 733 MET cc_start: 0.8912 (ptt) cc_final: 0.8640 (ptm) REVERT: D 796 ASP cc_start: 0.8282 (p0) cc_final: 0.8025 (p0) REVERT: D 1265 ASN cc_start: 0.8485 (m-40) cc_final: 0.8094 (m-40) outliers start: 67 outliers final: 31 residues processed: 357 average time/residue: 1.3933 time to fit residues: 574.4282 Evaluate side-chains 295 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 261 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 136 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 0.1980 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.0370 chunk 283 optimal weight: 0.9980 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 53 HIS A 100 GLN B 5 GLN B 79 ASN C 476 HIS C 603 ASN D 5 ASN D 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26478 Z= 0.215 Angle : 0.594 10.442 36348 Z= 0.316 Chirality : 0.043 0.182 4172 Planarity : 0.005 0.041 4401 Dihedral : 17.127 179.960 4702 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.39 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 12.32 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % 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 (0.15), residues: 3032 helix: 0.80 (0.16), residues: 1096 sheet: -0.35 (0.25), residues: 422 loop : -1.28 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 223 HIS 0.004 0.001 HIS C 200 PHE 0.012 0.001 PHE C 153 TYR 0.014 0.001 TYR A 168 ARG 0.008 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 306 time to evaluate : 2.933 Fit side-chains revert: symmetry clash REVERT: Z 125 ASN cc_start: 0.8561 (m-40) cc_final: 0.8282 (m-40) REVERT: A 137 GLU cc_start: 0.7980 (pp20) cc_final: 0.7706 (pp20) REVERT: B 2 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 188 ASP cc_start: 0.8201 (t0) cc_final: 0.7920 (t0) REVERT: C 172 GLU cc_start: 0.8282 (tt0) cc_final: 0.8023 (tt0) REVERT: C 336 GLU cc_start: 0.6718 (tp30) cc_final: 0.6458 (tp30) REVERT: C 393 MET cc_start: 0.8579 (mmt) cc_final: 0.8188 (mmt) REVERT: C 429 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6737 (tp30) REVERT: C 584 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7003 (ptp-110) REVERT: C 733 ASP cc_start: 0.8423 (m-30) cc_final: 0.8101 (m-30) REVERT: C 758 ASP cc_start: 0.8392 (p0) cc_final: 0.8121 (p0) REVERT: C 814 LEU cc_start: 0.1326 (OUTLIER) cc_final: 0.0751 (mm) REVERT: C 843 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C 853 PHE cc_start: 0.8201 (m-80) cc_final: 0.7982 (m-80) REVERT: C 947 ASP cc_start: 0.7623 (p0) cc_final: 0.7243 (p0) REVERT: D 177 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.3796 (mp) REVERT: D 215 GLU cc_start: 0.6769 (mp0) cc_final: 0.6548 (mp0) REVERT: D 541 MET cc_start: 0.9182 (mtm) cc_final: 0.8888 (mtm) REVERT: D 733 MET cc_start: 0.8870 (ptt) cc_final: 0.8631 (ptm) REVERT: D 796 ASP cc_start: 0.8115 (p0) cc_final: 0.7893 (p0) REVERT: D 1265 ASN cc_start: 0.8241 (m-40) cc_final: 0.7858 (m110) REVERT: E 36 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8587 (p) outliers start: 77 outliers final: 46 residues processed: 360 average time/residue: 1.3737 time to fit residues: 573.7621 Evaluate side-chains 310 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 259 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 306 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 407 GLN C 603 ASN C1066 GLN D 239 ASN D1125 GLN E 100 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26478 Z= 0.278 Angle : 0.597 9.407 36348 Z= 0.317 Chirality : 0.044 0.165 4172 Planarity : 0.005 0.045 4401 Dihedral : 17.039 179.756 4690 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.25 % Rotamer: Outliers : 4.47 % Allowed : 13.02 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % 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: -0.41 (0.15), residues: 3032 helix: 0.95 (0.16), residues: 1092 sheet: -0.13 (0.25), residues: 415 loop : -1.24 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 938 HIS 0.005 0.001 HIS C 479 PHE 0.021 0.002 PHE D 6 TYR 0.018 0.001 TYR A 168 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 283 time to evaluate : 2.761 Fit side-chains revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8584 (t) REVERT: A 89 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: A 137 GLU cc_start: 0.7906 (pp20) cc_final: 0.7630 (pp20) REVERT: A 197 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: B 34 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (pt) REVERT: B 188 ASP cc_start: 0.8234 (t0) cc_final: 0.7946 (t0) REVERT: C 259 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7209 (mpp80) REVERT: C 393 MET cc_start: 0.8580 (mmt) cc_final: 0.8151 (mmt) REVERT: C 429 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6811 (tp30) REVERT: C 558 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6882 (mtp85) REVERT: C 584 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7059 (ptp-110) REVERT: C 733 ASP cc_start: 0.8477 (m-30) cc_final: 0.8166 (m-30) REVERT: C 758 ASP cc_start: 0.8390 (p0) cc_final: 0.8140 (p0) REVERT: C 814 LEU cc_start: 0.1265 (OUTLIER) cc_final: 0.0778 (mm) REVERT: C 843 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 853 PHE cc_start: 0.8197 (m-80) cc_final: 0.7943 (m-80) REVERT: C 885 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8772 (mt) REVERT: C 947 ASP cc_start: 0.7577 (p0) cc_final: 0.7185 (p0) REVERT: C 982 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: D 177 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.3825 (mp) REVERT: D 236 VAL cc_start: 0.6876 (OUTLIER) cc_final: 0.6591 (m) REVERT: D 250 GLU cc_start: 0.7041 (tp30) cc_final: 0.6829 (mm-30) REVERT: D 339 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.7025 (t0) REVERT: D 733 MET cc_start: 0.8905 (ptt) cc_final: 0.8622 (ptm) REVERT: D 796 ASP cc_start: 0.8083 (p0) cc_final: 0.7789 (p0) REVERT: D 1076 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7680 (p) REVERT: D 1117 ASP cc_start: 0.7990 (p0) cc_final: 0.7773 (p0) REVERT: D 1265 ASN cc_start: 0.8257 (m-40) cc_final: 0.7873 (m110) REVERT: E 36 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (p) REVERT: E 70 GLN cc_start: 0.5243 (OUTLIER) cc_final: 0.4451 (tm-30) outliers start: 114 outliers final: 59 residues processed: 373 average time/residue: 1.3433 time to fit residues: 580.9595 Evaluate side-chains 336 residues out of total 2572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 892 GLN Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2627 > 50: distance: 7 - 12: 29.665 distance: 12 - 13: 15.129 distance: 13 - 14: 26.755 distance: 13 - 16: 16.037 distance: 14 - 15: 39.776 distance: 14 - 21: 4.801 distance: 16 - 17: 35.348 distance: 17 - 18: 31.492 distance: 18 - 19: 28.194 distance: 19 - 20: 18.073 distance: 21 - 22: 41.016 distance: 22 - 23: 5.395 distance: 23 - 24: 24.226 distance: 23 - 25: 5.603 distance: 25 - 26: 44.055 distance: 26 - 27: 18.692 distance: 27 - 28: 7.999 distance: 27 - 34: 39.972 distance: 29 - 30: 33.042 distance: 30 - 31: 6.099 distance: 31 - 32: 17.896 distance: 31 - 33: 40.904 distance: 35 - 36: 11.410 distance: 35 - 38: 33.714 distance: 36 - 37: 17.247 distance: 36 - 41: 42.919 distance: 38 - 39: 24.770 distance: 38 - 40: 52.773 distance: 41 - 42: 36.834 distance: 42 - 43: 36.977 distance: 42 - 45: 28.959 distance: 43 - 44: 26.414 distance: 43 - 50: 42.359 distance: 47 - 48: 13.788 distance: 47 - 49: 18.864 distance: 50 - 51: 56.743 distance: 51 - 52: 40.602 distance: 51 - 54: 49.909 distance: 52 - 53: 39.940 distance: 54 - 55: 10.894 distance: 55 - 56: 35.141 distance: 55 - 57: 15.855 distance: 59 - 60: 45.078 distance: 59 - 62: 19.115 distance: 60 - 61: 28.333 distance: 60 - 65: 37.427 distance: 61 - 90: 35.360 distance: 62 - 63: 5.187 distance: 62 - 64: 36.207 distance: 65 - 71: 17.058 distance: 66 - 69: 17.896 distance: 67 - 68: 13.628 distance: 68 - 98: 26.339 distance: 69 - 70: 16.536 distance: 70 - 71: 15.313 distance: 72 - 73: 11.044 distance: 73 - 74: 4.463 distance: 73 - 76: 31.443 distance: 74 - 75: 35.254 distance: 74 - 81: 9.679 distance: 75 - 106: 36.231 distance: 76 - 77: 34.237 distance: 77 - 78: 27.567 distance: 78 - 79: 24.262 distance: 78 - 80: 7.647 distance: 81 - 82: 33.081 distance: 82 - 83: 22.271 distance: 82 - 85: 40.992 distance: 83 - 84: 17.666 distance: 83 - 90: 30.343 distance: 84 - 114: 11.814 distance: 85 - 86: 17.973 distance: 86 - 87: 22.670 distance: 87 - 88: 6.047 distance: 87 - 89: 9.155