Starting phenix.real_space_refine on Tue Dec 12 01:35:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/12_2023/6s1n_10081_neut_updated.pdb" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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 Fe 4 7.16 5 Zn 1 6.06 5 P 53 5.49 5 S 125 5.16 5 C 12326 2.51 5 N 3377 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19726 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 8085 Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3304 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1130 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 7, 'TRANS': 58} Chain: "E" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1924 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "P" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Unusual residues: {'DOC': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' ZN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 98.895 98.577 74.641 1.00 40.62 S ATOM 7175 SG CYS A1015 101.836 96.664 76.373 1.00 40.62 S ATOM 7248 SG CYS A1026 102.565 100.377 75.449 1.00 40.62 S ATOM 7264 SG CYS A1029 101.561 98.148 72.827 1.00 40.62 S ATOM 7616 SG CYS A1071 59.269 81.282 75.051 1.00 40.62 S ATOM 7654 SG CYS A1076 63.753 77.569 73.723 1.00 30.94 S ATOM 7515 SG CYS A1058 63.215 83.861 70.771 1.00 40.62 S ATOM 7541 SG CYS A1061 59.419 78.748 69.874 1.00 24.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1100 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1100 " occ=0.50 Time building chain proxies: 13.85, per 1000 atoms: 0.70 Number of scatterers: 19726 At special positions: 0 Unit cell: (154.44, 129.6, 172.8, 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 1 29.99 Fe 4 26.01 S 125 16.00 P 53 15.00 O 3840 8.00 N 3377 7.00 C 12326 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 23 sheets defined 26.6% alpha, 21.2% beta 18 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 8.71 Creating SS restraints... Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.721A pdb=" N VAL A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA A 221 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Proline residue: A 222 - end of helix removed outlier: 4.150A pdb=" N LEU A 227 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 302 through 305 removed outlier: 3.593A pdb=" N GLN A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 502 through 525 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 656 through 676 removed outlier: 4.733A pdb=" N LYS A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 704 removed outlier: 3.886A pdb=" N TYR A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 738 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 838 through 852 Processing helix chain 'A' and resid 857 through 872 Processing helix chain 'A' and resid 899 through 905 Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.931A pdb=" N GLU A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 985 Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1034 through 1055 removed outlier: 4.885A pdb=" N GLU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A1052 " --> pdb=" O GLU A1048 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1053 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1078 through 1081 No H-bonds generated for 'chain 'A' and resid 1078 through 1081' Processing helix chain 'A' and resid 1084 through 1095 removed outlier: 3.567A pdb=" N GLN A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.695A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.901A pdb=" N GLN B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 223 Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.971A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 23 through 29 Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 113 through 123 removed outlier: 4.147A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 removed outlier: 3.668A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'E' and resid 10 through 17 Processing helix chain 'E' and resid 72 through 81 removed outlier: 4.224A pdb=" N CYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 Processing helix chain 'E' and resid 209 through 221 removed outlier: 3.557A pdb=" N LYS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR E 219 " --> pdb=" O PHE E 215 " (cutoff:3.500A) Proline residue: E 220 - end of helix Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.873A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 78 Processing helix chain 'F' and resid 141 through 153 removed outlier: 4.193A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.429A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.616A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 141 through 154 removed outlier: 3.591A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 221 removed outlier: 4.616A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.300A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE A 128 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 101 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 126 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N HIS A 103 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 124 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 286 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS A 140 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 288 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N HIS A 142 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 290 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 151 Processing sheet with id= C, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.914A pdb=" N GLY A 395 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 315 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 336 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS A 367 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR A 356 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 369 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 431 through 438 Processing sheet with id= E, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.982A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 792 through 798 removed outlier: 6.932A pdb=" N THR A 600 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 797 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 598 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 751 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= H, first strand: chain 'A' and resid 883 through 886 Processing sheet with id= I, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.653A pdb=" N GLU B 132 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 175 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 164 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 173 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 447 through 451 removed outlier: 7.725A pdb=" N LEU B 197 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL B 241 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 199 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 243 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B 243 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 293 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.608A pdb=" N VAL B 401 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR B 402 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 424 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 411 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 73 through 80 removed outlier: 5.730A pdb=" N LEU C 62 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL C 100 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER C 64 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE C 98 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= N, first strand: chain 'E' and resid 66 through 71 removed outlier: 7.299A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 203 through 208 removed outlier: 6.011A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= Q, first strand: chain 'F' and resid 25 through 28 Processing sheet with id= R, first strand: chain 'F' and resid 34 through 40 removed outlier: 5.608A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 203 through 208 Processing sheet with id= T, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.646A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 25 through 30 Processing sheet with id= V, first strand: chain 'G' and resid 34 through 40 removed outlier: 5.331A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.986A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 8.65 Time building geometry restraints manager: 8.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 7991 1.40 - 1.63: 12020 1.63 - 1.85: 187 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 20210 Sorted by residual: bond pdb=" C2' TTP T 101 " pdb=" C3' TTP T 101 " ideal model delta sigma weight residual 1.524 1.216 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" C4' DOC P 25 " pdb=" C3' DOC P 25 " ideal model delta sigma weight residual 1.334 1.521 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.609 1.431 0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.268 1.429 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C4' TTP T 101 " pdb=" O4' TTP T 101 " ideal model delta sigma weight residual 1.426 1.269 0.157 2.00e-02 2.50e+03 6.13e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 72.66 - 84.96: 12 84.96 - 97.26: 19 97.26 - 109.56: 3337 109.56 - 121.86: 19676 121.86 - 134.16: 4565 Bond angle restraints: 27609 Sorted by residual: angle pdb=" N ALA B 179 " pdb=" CA ALA B 179 " pdb=" C ALA B 179 " ideal model delta sigma weight residual 111.28 119.50 -8.22 1.09e+00 8.42e-01 5.69e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.66 7.70 1.09e+00 8.42e-01 4.98e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 119.03 -8.83 1.32e+00 5.74e-01 4.47e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.49 -7.21 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C PRO A 82 " pdb=" N THR A 83 " pdb=" CA THR A 83 " ideal model delta sigma weight residual 120.94 132.43 -11.49 1.90e+00 2.77e-01 3.66e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.55: 11279 27.55 - 55.10: 758 55.10 - 82.66: 122 82.66 - 110.21: 13 110.21 - 137.76: 2 Dihedral angle restraints: 12174 sinusoidal: 5211 harmonic: 6963 Sorted by residual: dihedral pdb=" C2 TTP T 101 " pdb=" C1' TTP T 101 " pdb=" N1 TTP T 101 " pdb=" O4' TTP T 101 " ideal model delta sinusoidal sigma weight residual 301.68 163.92 137.76 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CA HIS A1021 " pdb=" CB HIS A1021 " ideal model delta harmonic sigma weight residual 122.80 137.60 -14.80 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" C5' TTP T 101 " pdb=" O5' TTP T 101 " pdb=" PA TTP T 101 " pdb=" O3A TTP T 101 " ideal model delta sinusoidal sigma weight residual 179.97 65.22 114.75 1 2.00e+01 2.50e-03 3.40e+01 ... (remaining 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2832 0.100 - 0.200: 300 0.200 - 0.299: 17 0.299 - 0.399: 0 0.399 - 0.499: 3 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ASP B 180 " pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CB ASP B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA HIS A1021 " pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CB HIS A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CB ILE A1078 " pdb=" CA ILE A1078 " pdb=" CG1 ILE A1078 " pdb=" CG2 ILE A1078 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N AGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N BGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 1 " 0.015 2.00e-02 2.50e+03 1.81e-02 9.80e+00 pdb=" N9 DG T 1 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DG T 1 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DG T 1 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DG T 1 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DG T 1 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG T 1 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG T 1 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DG T 1 " 0.010 2.00e-02 2.50e+03 pdb=" N2 DG T 1 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG T 1 " -0.051 2.00e-02 2.50e+03 pdb=" C4 DG T 1 " 0.005 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 104 2.52 - 3.12: 12754 3.12 - 3.71: 28892 3.71 - 4.31: 40593 4.31 - 4.90: 67452 Nonbonded interactions: 149795 Sorted by model distance: nonbonded pdb=" C2' DA T 4 " pdb=" C7 DT T 5 " model vdw 1.929 3.860 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.930 3.860 nonbonded pdb=" OE1 GLN B 308 " pdb=" ND2 ASN B 330 " model vdw 1.954 2.520 nonbonded pdb=" O GLN B 308 " pdb=" CB THR B 329 " model vdw 2.044 3.470 nonbonded pdb=" CG1 VAL A 861 " pdb=" NE ARG A 985 " model vdw 2.074 3.540 ... (remaining 149790 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 'E' and (resid 1 through 107 or resid 109 through 185 or resid 191 or res \ id 194 through 255)) selection = (chain 'F' and (resid 1 through 191 or resid 194 through 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 185 or resid 193 through 255)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 10.430 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 70.030 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.308 20210 Z= 0.558 Angle : 1.128 11.491 27609 Z= 0.639 Chirality : 0.063 0.499 3152 Planarity : 0.009 0.075 3387 Dihedral : 18.021 137.760 7672 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 0.83 % Allowed : 8.79 % Favored : 90.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -3.47 (0.15), residues: 2370 helix: -2.39 (0.16), residues: 670 sheet: -0.89 (0.20), residues: 604 loop : -3.09 (0.15), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 344 HIS 0.011 0.002 HIS C 99 PHE 0.032 0.003 PHE A 637 TYR 0.025 0.003 TYR A 618 ARG 0.013 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 656 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 670 average time/residue: 0.3893 time to fit residues: 374.6980 Evaluate side-chains 340 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1960 time to fit residues: 3.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 285 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 480 HIS A 565 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 865 GLN A 880 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS A1066 HIS A1092 GLN B 49 GLN B 70 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 232 GLN B 285 GLN C 58 HIS D 103 HIS E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 125 GLN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 204 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20210 Z= 0.259 Angle : 0.756 9.444 27609 Z= 0.392 Chirality : 0.046 0.245 3152 Planarity : 0.007 0.094 3387 Dihedral : 15.747 159.787 3159 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -2.16 (0.16), residues: 2370 helix: -0.78 (0.19), residues: 663 sheet: -0.34 (0.20), residues: 617 loop : -2.55 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 28 HIS 0.006 0.001 HIS B 373 PHE 0.028 0.002 PHE B 431 TYR 0.019 0.002 TYR A 956 ARG 0.013 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.3327 time to fit residues: 203.5030 Evaluate side-chains 280 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 72.7469 > 50: distance: 40 - 43: 19.656 distance: 43 - 44: 38.078 distance: 44 - 45: 42.430 distance: 44 - 47: 7.224 distance: 45 - 46: 9.153 distance: 45 - 50: 32.900 distance: 47 - 48: 36.844 distance: 47 - 49: 36.822 distance: 50 - 51: 30.387 distance: 51 - 52: 13.938 distance: 51 - 54: 36.819 distance: 52 - 53: 14.757 distance: 52 - 61: 28.847 distance: 54 - 55: 37.214 distance: 55 - 56: 9.759 distance: 56 - 57: 44.015 distance: 57 - 58: 29.347 distance: 58 - 59: 40.354 distance: 58 - 60: 15.638 distance: 61 - 62: 39.649 distance: 62 - 65: 39.612 distance: 63 - 72: 48.344 distance: 65 - 66: 33.670 distance: 66 - 67: 34.938 distance: 67 - 68: 27.834 distance: 69 - 70: 31.681 distance: 69 - 71: 10.002 distance: 72 - 73: 28.359 distance: 73 - 74: 35.281 distance: 73 - 76: 44.226 distance: 74 - 80: 41.189 distance: 76 - 77: 35.584 distance: 77 - 78: 39.189 distance: 77 - 79: 23.024 distance: 80 - 81: 39.206 distance: 81 - 82: 46.207 distance: 81 - 84: 7.235 distance: 82 - 83: 15.875 distance: 82 - 88: 16.312 distance: 84 - 85: 37.977 distance: 85 - 86: 38.395 distance: 85 - 87: 61.264 distance: 89 - 90: 39.693 distance: 89 - 92: 21.636 distance: 90 - 91: 40.669 distance: 90 - 94: 40.746 distance: 92 - 93: 22.075 distance: 94 - 95: 39.407 distance: 94 - 100: 40.600 distance: 95 - 96: 35.340 distance: 96 - 97: 40.319 distance: 96 - 101: 53.673 distance: 97 - 121: 37.788 distance: 99 - 100: 56.538 distance: 101 - 102: 37.534 distance: 102 - 103: 10.846 distance: 103 - 104: 16.804 distance: 103 - 109: 46.632 distance: 104 - 129: 26.113 distance: 105 - 106: 56.439 distance: 106 - 107: 20.087 distance: 106 - 108: 38.874 distance: 109 - 110: 24.609 distance: 110 - 111: 12.233 distance: 110 - 113: 42.368 distance: 111 - 112: 11.120 distance: 111 - 116: 10.336 distance: 112 - 135: 27.987 distance: 113 - 114: 8.470 distance: 113 - 115: 50.607 distance: 116 - 117: 33.338 distance: 117 - 118: 20.490 distance: 117 - 120: 20.549 distance: 118 - 121: 34.314 distance: 119 - 142: 34.603