Starting phenix.real_space_refine on Mon Mar 18 03:17:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_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_10081/03_2024/6s1n_10081_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_10081_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1n_10081/03_2024/6s1n_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-dev-5265/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: 14.08, per 1000 atoms: 0.71 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: 7.82 Conformation dependent library (CDL) restraints added in 4.9 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: 9.18 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: 9.76 Time building geometry restraints manager: 8.44 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: 10.770 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: 0.000 Extract box with map and model: 10.050 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 72.800 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.020 ------------------------------------------------------------------------------- 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 : 1.953 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 REVERT: A 264 ASN cc_start: 0.7196 (t0) cc_final: 0.6912 (t0) REVERT: A 335 ILE cc_start: 0.7523 (pt) cc_final: 0.7220 (pt) REVERT: A 493 ILE cc_start: 0.8616 (mt) cc_final: 0.7657 (pt) REVERT: A 512 CYS cc_start: 0.8192 (t) cc_final: 0.7551 (t) REVERT: A 522 LEU cc_start: 0.7836 (mt) cc_final: 0.7620 (mt) REVERT: A 546 LEU cc_start: 0.6808 (mt) cc_final: 0.6372 (mt) REVERT: A 552 GLN cc_start: 0.7151 (mt0) cc_final: 0.6068 (mm-40) REVERT: A 612 MET cc_start: 0.7141 (mtt) cc_final: 0.6703 (mmt) REVERT: A 693 LEU cc_start: 0.8584 (mt) cc_final: 0.8201 (mt) REVERT: A 696 SER cc_start: 0.8531 (m) cc_final: 0.8020 (p) REVERT: A 1010 ASN cc_start: 0.5764 (m110) cc_final: 0.5465 (m-40) REVERT: A 1088 ASP cc_start: 0.8332 (m-30) cc_final: 0.7940 (t0) REVERT: A 1089 LEU cc_start: 0.8828 (tp) cc_final: 0.8625 (tt) REVERT: B 46 PHE cc_start: 0.7001 (m-80) cc_final: 0.6595 (m-80) REVERT: B 52 HIS cc_start: 0.8104 (m-70) cc_final: 0.7796 (m-70) REVERT: B 53 ILE cc_start: 0.8781 (mp) cc_final: 0.8321 (mm) REVERT: B 167 ASP cc_start: 0.7828 (m-30) cc_final: 0.7535 (p0) REVERT: B 296 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7002 (Cg_exo) REVERT: D 49 LEU cc_start: 0.8526 (mt) cc_final: 0.8177 (mm) REVERT: D 69 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7541 (ttt180) REVERT: E 47 LEU cc_start: 0.7176 (tt) cc_final: 0.6420 (tt) REVERT: E 75 MET cc_start: 0.7607 (tpp) cc_final: 0.7090 (mmm) REVERT: E 116 MET cc_start: 0.5758 (ttt) cc_final: 0.4661 (tpt) REVERT: F 52 LEU cc_start: 0.8779 (mt) cc_final: 0.8569 (mt) REVERT: F 87 ILE cc_start: 0.8266 (mt) cc_final: 0.7874 (mm) REVERT: F 88 ILE cc_start: 0.7034 (mt) cc_final: 0.6245 (mp) REVERT: F 146 ARG cc_start: 0.7326 (mmp80) cc_final: 0.6925 (mmm160) REVERT: G 121 LEU cc_start: 0.4821 (pt) cc_final: 0.4236 (tp) outliers start: 17 outliers final: 2 residues processed: 670 average time/residue: 0.3720 time to fit residues: 354.9339 Evaluate side-chains 349 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.3584 ------------------------------------------------------------------------------- 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 264 ASN ** 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 A1092 GLN B 49 GLN B 70 GLN B 184 GLN B 225 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN C 4 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: 0.5950 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 20210 Z= 0.275 Angle : 0.749 10.581 27609 Z= 0.388 Chirality : 0.046 0.248 3152 Planarity : 0.006 0.059 3387 Dihedral : 15.788 157.901 3159 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % 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: -0.75 (0.19), residues: 662 sheet: -0.34 (0.20), residues: 619 loop : -2.57 (0.16), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 28 HIS 0.006 0.001 HIS B 373 PHE 0.030 0.002 PHE B 431 TYR 0.021 0.002 TYR A 956 ARG 0.010 0.001 ARG B 62 *********************** 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 413 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 2.265 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: A 169 ASN cc_start: 0.7327 (m110) cc_final: 0.6443 (m110) REVERT: A 247 ASN cc_start: 0.7485 (p0) cc_final: 0.7231 (p0) REVERT: A 264 ASN cc_start: 0.6957 (t0) cc_final: 0.6681 (t0) REVERT: A 508 LEU cc_start: 0.9067 (tp) cc_final: 0.8489 (tp) REVERT: A 535 MET cc_start: 0.7807 (ttt) cc_final: 0.7532 (ttt) REVERT: A 552 GLN cc_start: 0.6983 (mt0) cc_final: 0.6730 (mm-40) REVERT: A 663 LEU cc_start: 0.8849 (mm) cc_final: 0.8547 (mp) REVERT: A 687 ASP cc_start: 0.8412 (t0) cc_final: 0.8119 (m-30) REVERT: A 696 SER cc_start: 0.8110 (m) cc_final: 0.7451 (p) REVERT: A 711 LEU cc_start: 0.7206 (tp) cc_final: 0.6914 (tp) REVERT: A 729 GLU cc_start: 0.8040 (mp0) cc_final: 0.7623 (mp0) REVERT: A 798 TYR cc_start: 0.5574 (m-10) cc_final: 0.5164 (m-80) REVERT: A 1088 ASP cc_start: 0.8690 (m-30) cc_final: 0.8447 (t0) REVERT: B 52 HIS cc_start: 0.8169 (m-70) cc_final: 0.7905 (m170) REVERT: B 92 CYS cc_start: 0.5461 (m) cc_final: 0.4802 (m) REVERT: B 94 VAL cc_start: 0.7908 (p) cc_final: 0.7699 (p) REVERT: B 131 ASP cc_start: 0.7306 (p0) cc_final: 0.6907 (p0) REVERT: B 167 ASP cc_start: 0.7732 (m-30) cc_final: 0.7438 (p0) REVERT: B 180 ASP cc_start: 0.4841 (m-30) cc_final: 0.4329 (m-30) REVERT: E 47 LEU cc_start: 0.7351 (tt) cc_final: 0.6679 (tt) REVERT: E 75 MET cc_start: 0.8055 (tpp) cc_final: 0.6249 (ttm) REVERT: E 84 ASN cc_start: 0.6019 (p0) cc_final: 0.5677 (p0) REVERT: F 24 ASN cc_start: 0.5596 (t0) cc_final: 0.5114 (t0) REVERT: F 146 ARG cc_start: 0.7640 (mmp80) cc_final: 0.7244 (mmm160) REVERT: F 195 VAL cc_start: 0.5925 (t) cc_final: 0.5595 (m) REVERT: F 199 MET cc_start: 0.2817 (tpp) cc_final: 0.1976 (mmm) REVERT: G 121 LEU cc_start: 0.5440 (pt) cc_final: 0.4665 (tp) REVERT: G 169 PHE cc_start: 0.6613 (m-10) cc_final: 0.6293 (m-10) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.3279 time to fit residues: 204.1373 Evaluate side-chains 300 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 149 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 chunk 195 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN B 225 GLN B 232 GLN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 125 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS G 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20210 Z= 0.225 Angle : 0.688 11.877 27609 Z= 0.355 Chirality : 0.045 0.218 3152 Planarity : 0.006 0.095 3387 Dihedral : 15.675 156.701 3159 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % 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: -1.57 (0.16), residues: 2370 helix: -0.14 (0.20), residues: 652 sheet: 0.03 (0.21), residues: 602 loop : -2.26 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.009 0.001 HIS B 250 PHE 0.035 0.002 PHE A 479 TYR 0.016 0.001 TYR G 211 ARG 0.012 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 3 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 402 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 396 time to evaluate : 2.467 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: A 264 ASN cc_start: 0.7108 (t0) cc_final: 0.6692 (t0) REVERT: A 431 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6517 (pt) REVERT: A 449 VAL cc_start: 0.8742 (t) cc_final: 0.8507 (m) REVERT: A 512 CYS cc_start: 0.7853 (m) cc_final: 0.7651 (m) REVERT: A 611 MET cc_start: 0.7784 (mtm) cc_final: 0.7474 (mtm) REVERT: A 612 MET cc_start: 0.8428 (mmm) cc_final: 0.7942 (mmm) REVERT: A 687 ASP cc_start: 0.8439 (t0) cc_final: 0.8109 (m-30) REVERT: A 696 SER cc_start: 0.8240 (m) cc_final: 0.7708 (p) REVERT: A 798 TYR cc_start: 0.5894 (m-10) cc_final: 0.4822 (m-80) REVERT: A 954 THR cc_start: 0.8299 (p) cc_final: 0.8062 (p) REVERT: A 1038 GLN cc_start: 0.5314 (OUTLIER) cc_final: 0.4747 (tt0) REVERT: A 1098 ARG cc_start: 0.7815 (ptm160) cc_final: 0.6600 (ttt-90) REVERT: B 1 MET cc_start: 0.7354 (mmm) cc_final: 0.6906 (mmm) REVERT: B 52 HIS cc_start: 0.8102 (m-70) cc_final: 0.7895 (m170) REVERT: B 92 CYS cc_start: 0.5269 (m) cc_final: 0.4627 (m) REVERT: B 131 ASP cc_start: 0.7664 (p0) cc_final: 0.7199 (p0) REVERT: B 200 SER cc_start: 0.7471 (p) cc_final: 0.7110 (t) REVERT: B 342 LEU cc_start: 0.6642 (tt) cc_final: 0.6384 (mp) REVERT: B 345 SER cc_start: 0.8556 (t) cc_final: 0.8314 (p) REVERT: B 360 ASP cc_start: 0.7739 (t70) cc_final: 0.7525 (t70) REVERT: C 11 ASP cc_start: 0.8347 (t0) cc_final: 0.8039 (t0) REVERT: C 129 CYS cc_start: 0.5875 (m) cc_final: 0.5531 (t) REVERT: E 47 LEU cc_start: 0.7223 (tt) cc_final: 0.6259 (tp) REVERT: E 75 MET cc_start: 0.7346 (tpp) cc_final: 0.6718 (mmm) REVERT: E 84 ASN cc_start: 0.6301 (p0) cc_final: 0.5922 (p0) REVERT: F 146 ARG cc_start: 0.7682 (mmp80) cc_final: 0.7336 (mmm160) REVERT: F 199 MET cc_start: 0.3364 (tpp) cc_final: 0.2099 (tpt) REVERT: G 121 LEU cc_start: 0.5483 (pt) cc_final: 0.4940 (tp) REVERT: G 229 MET cc_start: 0.3837 (pmm) cc_final: 0.2329 (pmm) outliers start: 6 outliers final: 0 residues processed: 402 average time/residue: 0.3271 time to fit residues: 197.6774 Evaluate side-chains 291 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 114 optimal weight: 0.0870 chunk 208 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 HIS ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 250 HIS B 285 GLN C 35 ASN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 213 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20210 Z= 0.180 Angle : 0.639 9.325 27609 Z= 0.328 Chirality : 0.043 0.192 3152 Planarity : 0.005 0.109 3387 Dihedral : 15.410 154.527 3159 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % 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: -1.25 (0.17), residues: 2370 helix: 0.05 (0.20), residues: 665 sheet: 0.31 (0.22), residues: 585 loop : -2.06 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 28 HIS 0.008 0.001 HIS A 103 PHE 0.024 0.002 PHE B 299 TYR 0.019 0.001 TYR A 739 ARG 0.019 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 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 377 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 375 time to evaluate : 2.125 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: A 264 ASN cc_start: 0.7188 (t0) cc_final: 0.6824 (t0) REVERT: A 535 MET cc_start: 0.8086 (ttt) cc_final: 0.7701 (ttt) REVERT: A 612 MET cc_start: 0.8454 (mmm) cc_final: 0.7999 (mmm) REVERT: A 687 ASP cc_start: 0.8469 (t0) cc_final: 0.8099 (m-30) REVERT: A 696 SER cc_start: 0.8345 (m) cc_final: 0.7715 (p) REVERT: A 1052 SER cc_start: 0.9106 (m) cc_final: 0.8787 (t) REVERT: A 1098 ARG cc_start: 0.7647 (ptm160) cc_final: 0.7060 (ptm160) REVERT: B 52 HIS cc_start: 0.8247 (m-70) cc_final: 0.7745 (m170) REVERT: B 92 CYS cc_start: 0.4893 (m) cc_final: 0.4393 (m) REVERT: B 180 ASP cc_start: 0.4989 (m-30) cc_final: 0.4595 (m-30) REVERT: B 200 SER cc_start: 0.7342 (p) cc_final: 0.6847 (t) REVERT: B 345 SER cc_start: 0.8634 (t) cc_final: 0.8409 (p) REVERT: C 11 ASP cc_start: 0.8450 (t0) cc_final: 0.8109 (t0) REVERT: C 100 VAL cc_start: 0.5686 (t) cc_final: 0.5376 (m) REVERT: C 129 CYS cc_start: 0.5691 (m) cc_final: 0.5370 (t) REVERT: E 47 LEU cc_start: 0.7438 (tt) cc_final: 0.6529 (tp) REVERT: E 84 ASN cc_start: 0.6009 (p0) cc_final: 0.5545 (p0) REVERT: F 146 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7266 (mmm160) REVERT: G 21 ASP cc_start: 0.7998 (t0) cc_final: 0.7789 (t0) REVERT: G 36 ASN cc_start: 0.6227 (p0) cc_final: 0.5630 (m-40) REVERT: G 121 LEU cc_start: 0.5386 (pt) cc_final: 0.4985 (tp) REVERT: G 229 MET cc_start: 0.4074 (pmm) cc_final: 0.2652 (pmm) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.3223 time to fit residues: 183.1600 Evaluate side-chains 292 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20210 Z= 0.262 Angle : 0.727 12.406 27609 Z= 0.375 Chirality : 0.046 0.241 3152 Planarity : 0.006 0.096 3387 Dihedral : 15.479 151.611 3159 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2370 helix: 0.12 (0.20), residues: 660 sheet: 0.25 (0.21), residues: 606 loop : -1.93 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 79 HIS 0.007 0.002 HIS A 103 PHE 0.025 0.002 PHE B 455 TYR 0.015 0.002 TYR F 249 ARG 0.008 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 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 367 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.105 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: A 264 ASN cc_start: 0.7698 (t0) cc_final: 0.7376 (t0) REVERT: A 512 CYS cc_start: 0.7820 (m) cc_final: 0.7573 (m) REVERT: A 517 TYR cc_start: 0.8225 (t80) cc_final: 0.7952 (t80) REVERT: A 535 MET cc_start: 0.8247 (ttt) cc_final: 0.7827 (ttt) REVERT: A 570 MET cc_start: 0.5368 (ppp) cc_final: 0.5083 (ptm) REVERT: A 612 MET cc_start: 0.8837 (mmm) cc_final: 0.8468 (mmm) REVERT: A 696 SER cc_start: 0.8515 (m) cc_final: 0.7979 (p) REVERT: A 715 GLU cc_start: 0.8508 (mp0) cc_final: 0.7726 (mm-30) REVERT: A 729 GLU cc_start: 0.7874 (mp0) cc_final: 0.7547 (mp0) REVERT: A 937 MET cc_start: 0.7009 (mmp) cc_final: 0.6600 (tpp) REVERT: A 1052 SER cc_start: 0.9253 (m) cc_final: 0.8883 (t) REVERT: B 52 HIS cc_start: 0.8499 (m-70) cc_final: 0.7993 (m170) REVERT: B 92 CYS cc_start: 0.5460 (m) cc_final: 0.4849 (m) REVERT: B 180 ASP cc_start: 0.5146 (m-30) cc_final: 0.4752 (m-30) REVERT: B 200 SER cc_start: 0.7723 (p) cc_final: 0.7498 (t) REVERT: B 305 THR cc_start: 0.8859 (p) cc_final: 0.8655 (p) REVERT: B 360 ASP cc_start: 0.8062 (t70) cc_final: 0.7661 (t70) REVERT: C 11 ASP cc_start: 0.8368 (t0) cc_final: 0.8078 (t0) REVERT: C 59 VAL cc_start: 0.6618 (m) cc_final: 0.5670 (p) REVERT: C 100 VAL cc_start: 0.6913 (t) cc_final: 0.6578 (m) REVERT: E 6 LEU cc_start: 0.6133 (mt) cc_final: 0.5827 (tp) REVERT: E 47 LEU cc_start: 0.7417 (tt) cc_final: 0.6445 (tp) REVERT: E 84 ASN cc_start: 0.6352 (p0) cc_final: 0.5743 (p0) REVERT: E 207 PHE cc_start: 0.5330 (m-80) cc_final: 0.5091 (m-80) REVERT: F 95 ASN cc_start: 0.7536 (p0) cc_final: 0.7206 (p0) REVERT: F 97 ASP cc_start: 0.6641 (p0) cc_final: 0.6221 (m-30) REVERT: F 146 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7517 (mmm160) REVERT: F 199 MET cc_start: 0.2408 (tpp) cc_final: 0.1736 (mmm) REVERT: G 229 MET cc_start: 0.4182 (pmm) cc_final: 0.2681 (pmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3233 time to fit residues: 179.9598 Evaluate side-chains 262 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 0.0050 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 285 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN E 213 ASN E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20210 Z= 0.203 Angle : 0.663 11.482 27609 Z= 0.339 Chirality : 0.044 0.193 3152 Planarity : 0.005 0.091 3387 Dihedral : 15.305 150.159 3159 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % 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: -1.02 (0.17), residues: 2370 helix: 0.26 (0.21), residues: 663 sheet: 0.25 (0.21), residues: 618 loop : -1.85 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.007 0.001 HIS A 103 PHE 0.050 0.002 PHE F 144 TYR 0.017 0.001 TYR F 249 ARG 0.008 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 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 345 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 2.422 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: A 340 LEU cc_start: 0.8990 (mm) cc_final: 0.8537 (mt) REVERT: A 481 PHE cc_start: 0.8265 (m-80) cc_final: 0.8004 (m-80) REVERT: A 535 MET cc_start: 0.8195 (ttt) cc_final: 0.7898 (ttt) REVERT: A 612 MET cc_start: 0.8561 (mmm) cc_final: 0.8250 (mmm) REVERT: A 696 SER cc_start: 0.8520 (m) cc_final: 0.8090 (p) REVERT: A 715 GLU cc_start: 0.8444 (mp0) cc_final: 0.7411 (mm-30) REVERT: A 729 GLU cc_start: 0.7957 (mp0) cc_final: 0.7358 (mp0) REVERT: A 1052 SER cc_start: 0.9277 (m) cc_final: 0.8883 (t) REVERT: B 52 HIS cc_start: 0.8348 (m-70) cc_final: 0.7774 (m170) REVERT: B 61 MET cc_start: 0.7365 (mtp) cc_final: 0.7130 (mtp) REVERT: B 180 ASP cc_start: 0.5153 (m-30) cc_final: 0.4738 (m-30) REVERT: B 360 ASP cc_start: 0.8060 (t70) cc_final: 0.7765 (t0) REVERT: C 11 ASP cc_start: 0.8405 (t0) cc_final: 0.7656 (t0) REVERT: C 46 GLU cc_start: 0.8101 (tt0) cc_final: 0.7829 (mm-30) REVERT: C 51 GLU cc_start: 0.8678 (pt0) cc_final: 0.8366 (pt0) REVERT: C 59 VAL cc_start: 0.7112 (m) cc_final: 0.6224 (p) REVERT: E 6 LEU cc_start: 0.6146 (mt) cc_final: 0.5896 (tp) REVERT: E 47 LEU cc_start: 0.7415 (tt) cc_final: 0.6328 (tp) REVERT: E 84 ASN cc_start: 0.6271 (p0) cc_final: 0.5650 (p0) REVERT: E 207 PHE cc_start: 0.4927 (m-80) cc_final: 0.4590 (m-80) REVERT: F 95 ASN cc_start: 0.7567 (p0) cc_final: 0.7242 (p0) REVERT: F 146 ARG cc_start: 0.8090 (mmp80) cc_final: 0.7430 (mmm160) REVERT: G 36 ASN cc_start: 0.6013 (p0) cc_final: 0.5741 (p0) REVERT: G 229 MET cc_start: 0.4282 (pmm) cc_final: 0.2847 (pmm) outliers start: 2 outliers final: 0 residues processed: 345 average time/residue: 0.3136 time to fit residues: 166.5884 Evaluate side-chains 251 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 9.9990 chunk 26 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN A 948 HIS ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 20210 Z= 0.332 Angle : 0.807 18.060 27609 Z= 0.414 Chirality : 0.048 0.232 3152 Planarity : 0.006 0.105 3387 Dihedral : 15.519 147.012 3159 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.55 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.17), residues: 2370 helix: -0.21 (0.20), residues: 658 sheet: 0.04 (0.21), residues: 585 loop : -1.98 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 79 HIS 0.009 0.002 HIS B 250 PHE 0.038 0.003 PHE B 299 TYR 0.021 0.003 TYR F 249 ARG 0.010 0.001 ARG A 908 *********************** REFINEMENT MACRO_CYCLE 7 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 339 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.703 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: A 317 ILE cc_start: 0.7957 (pt) cc_final: 0.7665 (pt) REVERT: A 340 LEU cc_start: 0.9030 (mm) cc_final: 0.8704 (mt) REVERT: A 512 CYS cc_start: 0.7578 (m) cc_final: 0.7378 (m) REVERT: A 517 TYR cc_start: 0.8444 (t80) cc_final: 0.8122 (t80) REVERT: A 535 MET cc_start: 0.8250 (ttt) cc_final: 0.7926 (mmp) REVERT: A 612 MET cc_start: 0.8901 (mmm) cc_final: 0.8336 (mmm) REVERT: A 729 GLU cc_start: 0.7962 (mp0) cc_final: 0.7557 (mp0) REVERT: A 847 SER cc_start: 0.8736 (m) cc_final: 0.8317 (p) REVERT: B 52 HIS cc_start: 0.8487 (m-70) cc_final: 0.7929 (m170) REVERT: B 61 MET cc_start: 0.7538 (mtp) cc_final: 0.7215 (mtp) REVERT: B 180 ASP cc_start: 0.5393 (m-30) cc_final: 0.4849 (m-30) REVERT: B 213 LEU cc_start: 0.9036 (mt) cc_final: 0.8644 (mt) REVERT: B 305 THR cc_start: 0.9061 (p) cc_final: 0.8765 (p) REVERT: C 8 GLU cc_start: 0.8790 (tp30) cc_final: 0.8150 (tp30) REVERT: C 11 ASP cc_start: 0.8392 (t0) cc_final: 0.7922 (t0) REVERT: C 36 GLN cc_start: 0.7638 (tp40) cc_final: 0.6251 (tp40) REVERT: C 51 GLU cc_start: 0.9019 (pt0) cc_final: 0.8761 (pt0) REVERT: C 59 VAL cc_start: 0.8193 (m) cc_final: 0.7674 (p) REVERT: E 47 LEU cc_start: 0.7505 (tt) cc_final: 0.6450 (tp) REVERT: E 84 ASN cc_start: 0.6487 (p0) cc_final: 0.5910 (p0) REVERT: E 207 PHE cc_start: 0.5654 (m-80) cc_final: 0.5282 (m-80) REVERT: F 146 ARG cc_start: 0.8248 (mmp80) cc_final: 0.7768 (mmm160) REVERT: F 199 MET cc_start: 0.2567 (mmm) cc_final: 0.2091 (mmm) REVERT: G 126 LEU cc_start: 0.4417 (tt) cc_final: 0.3878 (mm) REVERT: G 229 MET cc_start: 0.4143 (pmm) cc_final: 0.2638 (pmm) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3169 time to fit residues: 165.6640 Evaluate side-chains 266 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 211 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.8923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20210 Z= 0.193 Angle : 0.678 10.594 27609 Z= 0.344 Chirality : 0.045 0.188 3152 Planarity : 0.005 0.090 3387 Dihedral : 15.336 145.112 3159 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.17 (0.17), residues: 2370 helix: 0.11 (0.20), residues: 659 sheet: 0.16 (0.21), residues: 594 loop : -1.88 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 28 HIS 0.007 0.001 HIS A 103 PHE 0.029 0.002 PHE B 299 TYR 0.017 0.001 TYR G 211 ARG 0.008 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 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 351 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.296 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: A 317 ILE cc_start: 0.7920 (pt) cc_final: 0.7508 (pt) REVERT: A 512 CYS cc_start: 0.7743 (m) cc_final: 0.7301 (m) REVERT: A 513 LEU cc_start: 0.9389 (pp) cc_final: 0.8807 (pp) REVERT: A 535 MET cc_start: 0.8295 (ttt) cc_final: 0.7775 (mmp) REVERT: A 612 MET cc_start: 0.8601 (mmm) cc_final: 0.8361 (mmm) REVERT: A 729 GLU cc_start: 0.7802 (mp0) cc_final: 0.7418 (mp0) REVERT: A 801 TYR cc_start: 0.5758 (t80) cc_final: 0.5456 (t80) REVERT: A 847 SER cc_start: 0.8522 (m) cc_final: 0.8142 (p) REVERT: A 962 LEU cc_start: 0.8665 (mt) cc_final: 0.8347 (mt) REVERT: A 1052 SER cc_start: 0.9337 (m) cc_final: 0.8865 (t) REVERT: A 1054 LEU cc_start: 0.9368 (mt) cc_final: 0.9148 (mt) REVERT: B 52 HIS cc_start: 0.8485 (m-70) cc_final: 0.7995 (m170) REVERT: B 61 MET cc_start: 0.7445 (mtp) cc_final: 0.7162 (mtp) REVERT: B 99 LYS cc_start: 0.8157 (tttm) cc_final: 0.7757 (tptt) REVERT: B 101 MET cc_start: 0.8248 (mmp) cc_final: 0.7231 (mmp) REVERT: B 180 ASP cc_start: 0.4820 (m-30) cc_final: 0.4457 (m-30) REVERT: B 213 LEU cc_start: 0.9115 (mt) cc_final: 0.8900 (mt) REVERT: C 8 GLU cc_start: 0.8840 (tp30) cc_final: 0.8129 (tp30) REVERT: C 11 ASP cc_start: 0.8314 (t0) cc_final: 0.7844 (t0) REVERT: C 36 GLN cc_start: 0.7544 (tp40) cc_final: 0.6381 (tp40) REVERT: C 51 GLU cc_start: 0.8668 (pt0) cc_final: 0.8440 (pt0) REVERT: D 67 LEU cc_start: 0.8047 (tp) cc_final: 0.7788 (tp) REVERT: E 47 LEU cc_start: 0.7419 (tt) cc_final: 0.6367 (tp) REVERT: E 84 ASN cc_start: 0.6515 (p0) cc_final: 0.5971 (p0) REVERT: E 207 PHE cc_start: 0.5346 (m-80) cc_final: 0.5109 (m-80) REVERT: F 146 ARG cc_start: 0.7919 (mmp80) cc_final: 0.7611 (mmm160) REVERT: F 199 MET cc_start: 0.2511 (mmm) cc_final: 0.2181 (mmm) REVERT: G 229 MET cc_start: 0.4695 (pmm) cc_final: 0.3594 (pmm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3115 time to fit residues: 167.6033 Evaluate side-chains 269 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.9553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20210 Z= 0.273 Angle : 0.733 11.610 27609 Z= 0.374 Chirality : 0.047 0.207 3152 Planarity : 0.006 0.089 3387 Dihedral : 15.340 142.664 3159 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -1.31 (0.17), residues: 2370 helix: -0.03 (0.20), residues: 670 sheet: 0.02 (0.21), residues: 585 loop : -1.91 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 28 HIS 0.008 0.002 HIS A 103 PHE 0.023 0.002 PHE A 199 TYR 0.029 0.002 TYR A 517 ARG 0.010 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 9 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 336 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.398 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: A 317 ILE cc_start: 0.7891 (pt) cc_final: 0.7613 (pt) REVERT: A 340 LEU cc_start: 0.8896 (mm) cc_final: 0.8601 (tp) REVERT: A 513 LEU cc_start: 0.9431 (pp) cc_final: 0.8966 (pp) REVERT: A 535 MET cc_start: 0.8363 (ttt) cc_final: 0.7679 (mmp) REVERT: A 612 MET cc_start: 0.8755 (mmm) cc_final: 0.8509 (mmm) REVERT: A 727 MET cc_start: 0.8880 (tmm) cc_final: 0.8525 (tmm) REVERT: A 729 GLU cc_start: 0.7736 (mp0) cc_final: 0.7369 (mp0) REVERT: A 847 SER cc_start: 0.8645 (m) cc_final: 0.8268 (p) REVERT: A 962 LEU cc_start: 0.8696 (mt) cc_final: 0.8489 (mt) REVERT: A 1048 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8457 (tp30) REVERT: A 1052 SER cc_start: 0.9373 (m) cc_final: 0.8821 (t) REVERT: B 52 HIS cc_start: 0.8555 (m-70) cc_final: 0.8099 (m170) REVERT: B 61 MET cc_start: 0.7578 (mtp) cc_final: 0.7325 (mtp) REVERT: B 180 ASP cc_start: 0.5140 (m-30) cc_final: 0.4551 (m-30) REVERT: B 213 LEU cc_start: 0.9001 (mt) cc_final: 0.8762 (mt) REVERT: B 358 MET cc_start: 0.5673 (ttp) cc_final: 0.5126 (ptm) REVERT: B 375 SER cc_start: 0.8934 (t) cc_final: 0.8716 (t) REVERT: C 8 GLU cc_start: 0.8863 (tp30) cc_final: 0.8195 (tp30) REVERT: C 11 ASP cc_start: 0.8383 (t0) cc_final: 0.7787 (t0) REVERT: C 23 TYR cc_start: 0.7548 (p90) cc_final: 0.7175 (p90) REVERT: C 36 GLN cc_start: 0.7491 (tp40) cc_final: 0.6217 (tp-100) REVERT: C 40 MET cc_start: 0.8029 (ptp) cc_final: 0.6610 (ptt) REVERT: E 47 LEU cc_start: 0.7549 (tt) cc_final: 0.6444 (tp) REVERT: E 84 ASN cc_start: 0.6476 (p0) cc_final: 0.5960 (p0) REVERT: E 207 PHE cc_start: 0.5632 (m-80) cc_final: 0.5327 (m-80) REVERT: F 139 MET cc_start: 0.6573 (mmp) cc_final: 0.6227 (mmp) REVERT: F 199 MET cc_start: 0.2810 (mmm) cc_final: 0.2492 (mmm) REVERT: G 68 MET cc_start: 0.7202 (mmm) cc_final: 0.6861 (mmm) REVERT: G 169 PHE cc_start: 0.6438 (m-10) cc_final: 0.6039 (m-10) REVERT: G 229 MET cc_start: 0.4246 (pmm) cc_final: 0.2959 (pmm) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3012 time to fit residues: 156.4589 Evaluate side-chains 267 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS F 38 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.9737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20210 Z= 0.215 Angle : 0.690 14.117 27609 Z= 0.350 Chirality : 0.045 0.189 3152 Planarity : 0.005 0.094 3387 Dihedral : 15.296 140.653 3159 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.24 (0.17), residues: 2370 helix: 0.01 (0.20), residues: 662 sheet: 0.05 (0.21), residues: 594 loop : -1.85 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 367 HIS 0.006 0.001 HIS A 103 PHE 0.034 0.002 PHE B 299 TYR 0.029 0.002 TYR A 517 ARG 0.007 0.001 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 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 331 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.949 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: A 340 LEU cc_start: 0.8907 (mm) cc_final: 0.8487 (tp) REVERT: A 535 MET cc_start: 0.8273 (ttt) cc_final: 0.7552 (mmp) REVERT: A 612 MET cc_start: 0.8669 (mmm) cc_final: 0.8435 (mmm) REVERT: A 715 GLU cc_start: 0.8772 (mp0) cc_final: 0.8159 (pm20) REVERT: A 729 GLU cc_start: 0.7667 (mp0) cc_final: 0.7321 (mp0) REVERT: A 801 TYR cc_start: 0.5949 (t80) cc_final: 0.5391 (t80) REVERT: A 847 SER cc_start: 0.8528 (m) cc_final: 0.8182 (p) REVERT: A 1052 SER cc_start: 0.9397 (m) cc_final: 0.8759 (t) REVERT: B 52 HIS cc_start: 0.8550 (m-70) cc_final: 0.8032 (m170) REVERT: B 61 MET cc_start: 0.7568 (mtp) cc_final: 0.7329 (mtp) REVERT: B 180 ASP cc_start: 0.5186 (m-30) cc_final: 0.4564 (m-30) REVERT: B 213 LEU cc_start: 0.9136 (mt) cc_final: 0.8723 (mt) REVERT: B 305 THR cc_start: 0.8965 (p) cc_final: 0.8751 (p) REVERT: B 375 SER cc_start: 0.8821 (t) cc_final: 0.8477 (t) REVERT: C 8 GLU cc_start: 0.8893 (tp30) cc_final: 0.8199 (tp30) REVERT: C 11 ASP cc_start: 0.8359 (t0) cc_final: 0.7748 (t0) REVERT: C 23 TYR cc_start: 0.7644 (p90) cc_final: 0.7335 (p90) REVERT: C 36 GLN cc_start: 0.7399 (tp40) cc_final: 0.6320 (tp-100) REVERT: C 40 MET cc_start: 0.8039 (ptp) cc_final: 0.6532 (ptt) REVERT: C 51 GLU cc_start: 0.8900 (pt0) cc_final: 0.8641 (pt0) REVERT: E 47 LEU cc_start: 0.7453 (tt) cc_final: 0.6370 (tp) REVERT: E 68 MET cc_start: 0.5659 (pmm) cc_final: 0.5316 (pmm) REVERT: E 84 ASN cc_start: 0.6553 (p0) cc_final: 0.6048 (p0) REVERT: E 207 PHE cc_start: 0.5600 (m-80) cc_final: 0.5284 (m-80) REVERT: F 146 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7851 (mmm160) REVERT: F 199 MET cc_start: 0.2793 (mmm) cc_final: 0.2548 (mmm) REVERT: G 40 MET cc_start: 0.5834 (tmm) cc_final: 0.5490 (tmm) REVERT: G 169 PHE cc_start: 0.6288 (m-10) cc_final: 0.5872 (m-10) REVERT: G 229 MET cc_start: 0.4540 (pmm) cc_final: 0.3523 (pmm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.3076 time to fit residues: 157.5444 Evaluate side-chains 262 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 191 optimal weight: 0.2980 chunk 80 optimal weight: 0.0870 chunk 196 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 246 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.094092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075592 restraints weight = 112397.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077430 restraints weight = 75833.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.078771 restraints weight = 55431.924| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.9824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20210 Z= 0.173 Angle : 0.659 12.610 27609 Z= 0.331 Chirality : 0.044 0.203 3152 Planarity : 0.005 0.077 3387 Dihedral : 15.113 140.521 3159 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.06 (0.17), residues: 2370 helix: 0.20 (0.20), residues: 665 sheet: 0.20 (0.21), residues: 592 loop : -1.80 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 367 HIS 0.006 0.001 HIS A 103 PHE 0.021 0.001 PHE F 215 TYR 0.028 0.001 TYR A 517 ARG 0.006 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4507.57 seconds wall clock time: 83 minutes 11.04 seconds (4991.04 seconds total)