Starting phenix.real_space_refine on Mon Mar 18 20:39:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnz_10540/03_2024/6tnz_10540_neut_updated.pdb" } resolution = 4.05 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= 0.001 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 138 5.16 5 C 13762 2.51 5 N 3773 2.21 5 O 4277 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 TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H GLU 258": "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: 22008 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: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2282 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' ZN': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 49.935 80.376 108.380 1.00 40.62 S ATOM 7175 SG CYS A1015 52.994 80.952 110.751 1.00 40.62 S ATOM 7248 SG CYS A1026 49.548 80.568 112.525 1.00 40.62 S ATOM 7264 SG CYS A1029 50.117 83.298 109.946 1.00 40.62 S ATOM 7616 SG CYS A1071 56.907 69.988 66.993 1.00 40.62 S ATOM 7654 SG CYS A1076 60.245 74.421 69.196 1.00 30.94 S ATOM 7515 SG CYS A1058 53.360 74.155 70.247 1.00 40.62 S ATOM 7541 SG CYS A1061 56.466 75.272 64.727 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: 15.54, per 1000 atoms: 0.71 Number of scatterers: 22008 At special positions: 0 Unit cell: (150.51, 153.99, 151.38, 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 138 16.00 P 53 15.00 O 4277 8.00 N 3773 7.00 C 13762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.33 Conformation dependent library (CDL) restraints added in 5.4 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 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 25 sheets defined 28.2% alpha, 19.7% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 9.57 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: 3.720A 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: 3.592A 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: 4.067A 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: 3.841A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.559A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.970A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.721A 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: 4.146A 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: 4.225A 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: 3.558A 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 17 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: 3.842A 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: 5.544A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'H' and resid 6 through 13 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 23 through 26 Processing helix chain 'H' and resid 35 through 43 Processing helix chain 'H' and resid 62 through 76 removed outlier: 4.389A pdb=" N MET H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR H 71 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 removed outlier: 4.454A pdb=" N ALA H 98 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 99 " --> pdb=" O GLU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 139 No H-bonds generated for 'chain 'H' and resid 136 through 139' Processing helix chain 'H' and resid 141 through 144 No H-bonds generated for 'chain 'H' and resid 141 through 144' Processing helix chain 'H' and resid 159 through 169 removed outlier: 3.899A pdb=" N ALA H 169 " --> pdb=" O ALA H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 184 Processing helix chain 'H' and resid 209 through 215 removed outlier: 3.724A pdb=" N GLN H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 231 removed outlier: 3.564A pdb=" N LEU H 226 " --> pdb=" O GLN H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 252 removed outlier: 3.585A pdb=" N VAL H 247 " --> pdb=" O PRO H 243 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 262 removed outlier: 3.995A pdb=" N ARG H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 318 through 330 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: 6.688A pdb=" N PHE A 128 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.541A 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: 5.113A pdb=" N HIS A 103 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 124 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.266A 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: 6.659A pdb=" N ALA A 288 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N HIS A 142 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.269A 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: 3.897A pdb=" N PHE A 315 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 336 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 6.326A 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: 6.615A 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: 6.981A 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: 6.933A pdb=" N THR A 600 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.798A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.504A 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: 3.652A 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: 7.591A 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: 7.720A pdb=" N VAL B 199 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 243 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 243 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 6.208A 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: 6.607A pdb=" N VAL B 401 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 402 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 6.444A 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: 5.731A pdb=" N LEU C 62 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL C 100 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER C 64 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.867A 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: 7.298A 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: 4.765A 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: 4.433A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.186A 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: 6.012A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.903A 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: 7.422A 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: 5.330A 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: 5.985A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 18 through 21 Processing sheet with id= Y, first strand: chain 'H' and resid 174 through 176 removed outlier: 3.927A pdb=" N ALA H 174 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS H 80 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE H 33 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL H 82 " --> pdb=" O ILE H 33 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 9.30 Time building geometry restraints manager: 9.11 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: 8934 1.40 - 1.63: 13377 1.63 - 1.85: 209 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 22532 Sorted by residual: bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.609 1.278 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" C2' TTP A1203 " pdb=" C3' TTP A1203 " ideal model delta sigma weight residual 1.524 1.216 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.268 1.551 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C4' DOC P 25 " pdb=" C3' DOC P 25 " ideal model delta sigma weight residual 1.334 1.615 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C3' DOC P 25 " pdb=" C2' DOC P 25 " ideal model delta sigma weight residual 1.489 1.306 0.183 2.00e-02 2.50e+03 8.41e+01 ... (remaining 22527 not shown) Histogram of bond angle deviations from ideal: 72.63 - 84.93: 12 84.93 - 97.24: 0 97.24 - 109.54: 3674 109.54 - 121.85: 21905 121.85 - 134.15: 5159 Bond angle restraints: 30750 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 111.28 119.43 -8.15 1.09e+00 8.42e-01 5.58e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.74 7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ILE H 241 " pdb=" CA ILE H 241 " pdb=" C ILE H 241 " ideal model delta sigma weight residual 109.51 119.40 -9.89 1.43e+00 4.89e-01 4.78e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 118.98 -8.78 1.32e+00 5.74e-01 4.43e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.45 -7.17 1.09e+00 8.42e-01 4.32e+01 ... (remaining 30745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.55: 12661 27.55 - 55.09: 836 55.09 - 82.64: 82 82.64 - 110.19: 15 110.19 - 137.73: 2 Dihedral angle restraints: 13596 sinusoidal: 5750 harmonic: 7846 Sorted by residual: dihedral pdb=" C2 TTP A1203 " pdb=" C1' TTP A1203 " pdb=" N1 TTP A1203 " pdb=" O4' TTP A1203 " ideal model delta sinusoidal sigma weight residual 301.68 163.95 137.73 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 122.80 137.58 -14.78 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" C5' TTP A1203 " pdb=" O5' TTP A1203 " pdb=" PA TTP A1203 " pdb=" O3A TTP A1203 " ideal model delta sinusoidal sigma weight residual 179.97 65.25 114.72 1 2.00e+01 2.50e-03 3.40e+01 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3073 0.098 - 0.196: 399 0.196 - 0.295: 32 0.295 - 0.393: 2 0.393 - 0.491: 3 Chirality restraints: 3509 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 2.02 0.49 2.00e-01 2.50e+01 6.02e+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 5.98e+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 4.09e+00 ... (remaining 3506 not shown) Planarity restraints: 3799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+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 4.58e-02 2.10e+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=" CB TYR H 173 " -0.058 2.00e-02 2.50e+03 3.20e-02 2.05e+01 pdb=" CG TYR H 173 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR H 173 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 173 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR H 173 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR H 173 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 173 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR H 173 " -0.052 2.00e-02 2.50e+03 ... (remaining 3796 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 114 2.48 - 3.08: 13611 3.08 - 3.69: 32061 3.69 - 4.29: 46457 4.29 - 4.90: 76489 Nonbonded interactions: 168732 Sorted by model distance: nonbonded pdb=" O GLN E 125 " pdb=" N GLY H 348 " model vdw 1.874 2.520 nonbonded pdb=" O ASP E 232 " pdb=" CE1 PHE H 343 " model vdw 1.921 3.340 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.985 3.860 nonbonded pdb=" SG CYS E 27 " pdb=" CG LEU H 350 " model vdw 2.016 3.830 nonbonded pdb=" N LEU E 121 " pdb=" OG SER H 352 " model vdw 2.056 2.520 ... (remaining 168727 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 13.980 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 77.930 Find NCS groups from input model: 1.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 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 0.331 22532 Z= 0.555 Angle : 1.136 11.465 30750 Z= 0.660 Chirality : 0.067 0.491 3509 Planarity : 0.008 0.075 3799 Dihedral : 17.555 137.735 8520 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.84 % Favored : 91.08 % Rotamer: Outliers : 1.57 % Allowed : 8.95 % Favored : 89.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -3.76 (0.14), residues: 2670 helix: -2.76 (0.14), residues: 799 sheet: -1.00 (0.20), residues: 630 loop : -3.12 (0.14), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 344 HIS 0.011 0.002 HIS C 99 PHE 0.032 0.004 PHE A 637 TYR 0.058 0.004 TYR H 173 ARG 0.013 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 364 time to evaluate : 2.822 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: A 391 ASP cc_start: 0.8275 (m-30) cc_final: 0.7995 (m-30) REVERT: E 35 VAL cc_start: 0.6311 (t) cc_final: 0.5575 (t) REVERT: E 47 LEU cc_start: 0.8010 (tt) cc_final: 0.7445 (mt) outliers start: 36 outliers final: 6 residues processed: 393 average time/residue: 0.3814 time to fit residues: 220.8465 Evaluate side-chains 173 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 212 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 558 GLN A 726 GLN A 842 ASN A 865 GLN A 948 HIS A 955 GLN A1038 GLN A1066 HIS A1092 GLN B 21 ASN B 49 GLN B 70 GLN B 140 GLN B 285 GLN C 58 HIS C 116 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS G 204 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 77 ASN H 222 GLN H 253 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 22532 Z= 0.262 Angle : 0.720 9.808 30750 Z= 0.373 Chirality : 0.045 0.260 3509 Planarity : 0.006 0.060 3799 Dihedral : 14.638 142.969 3482 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -2.38 (0.15), residues: 2670 helix: -1.00 (0.18), residues: 809 sheet: -0.47 (0.20), residues: 643 loop : -2.64 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 274 HIS 0.011 0.001 HIS H 276 PHE 0.029 0.002 PHE H 42 TYR 0.024 0.002 TYR H 26 ARG 0.007 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASP cc_start: 0.8339 (m-30) cc_final: 0.8032 (m-30) REVERT: E 119 MET cc_start: 0.4062 (pmm) cc_final: 0.3755 (pmm) REVERT: E 229 MET cc_start: 0.3861 (mpp) cc_final: 0.2534 (ttp) REVERT: F 199 MET cc_start: 0.7152 (tpp) cc_final: 0.6913 (tpp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3301 time to fit residues: 106.6122 Evaluate side-chains 133 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 219 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS B 184 GLN D 91 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 184 GLN G 49 GLN G 71 ASN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 22532 Z= 0.340 Angle : 0.758 10.445 30750 Z= 0.394 Chirality : 0.047 0.197 3509 Planarity : 0.006 0.073 3799 Dihedral : 14.653 136.218 3482 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.64 % Favored : 93.25 % Rotamer: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.91 (0.15), residues: 2670 helix: -0.28 (0.18), residues: 796 sheet: -0.41 (0.19), residues: 666 loop : -2.48 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 274 HIS 0.008 0.002 HIS C 72 PHE 0.019 0.002 PHE A 786 TYR 0.027 0.002 TYR A1080 ARG 0.009 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 MET cc_start: 0.7059 (mmm) cc_final: 0.6803 (mmm) REVERT: E 199 MET cc_start: 0.2742 (tpp) cc_final: 0.2415 (tpp) REVERT: H 67 MET cc_start: 0.1989 (tpp) cc_final: 0.1580 (ttt) outliers start: 3 outliers final: 0 residues processed: 176 average time/residue: 0.3154 time to fit residues: 89.5466 Evaluate side-chains 123 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 261 optimal weight: 0.0270 chunk 129 optimal weight: 0.2980 chunk 234 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN F 44 HIS ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22532 Z= 0.209 Angle : 0.628 9.717 30750 Z= 0.324 Chirality : 0.044 0.194 3509 Planarity : 0.005 0.054 3799 Dihedral : 14.270 137.845 3482 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.46 (0.16), residues: 2670 helix: 0.28 (0.19), residues: 801 sheet: -0.25 (0.20), residues: 662 loop : -2.29 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 28 HIS 0.005 0.001 HIS F 44 PHE 0.012 0.001 PHE A 148 TYR 0.017 0.001 TYR A1080 ARG 0.005 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 MET cc_start: 0.8238 (tpp) cc_final: 0.7780 (mmt) REVERT: E 229 MET cc_start: 0.4165 (mpp) cc_final: 0.3784 (mpp) REVERT: H 67 MET cc_start: 0.1676 (tpp) cc_final: 0.1204 (ttt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3230 time to fit residues: 83.3786 Evaluate side-chains 121 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 22532 Z= 0.360 Angle : 0.767 11.934 30750 Z= 0.396 Chirality : 0.047 0.231 3509 Planarity : 0.006 0.080 3799 Dihedral : 14.593 135.549 3482 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.65 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.79 (0.16), residues: 2670 helix: -0.14 (0.18), residues: 823 sheet: -0.42 (0.19), residues: 653 loop : -2.42 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 79 HIS 0.011 0.002 HIS A 160 PHE 0.022 0.002 PHE A1099 TYR 0.022 0.002 TYR G 133 ARG 0.014 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 772 MET cc_start: 0.8359 (tpp) cc_final: 0.8064 (mmt) REVERT: B 295 MET cc_start: 0.6426 (mtm) cc_final: 0.6132 (mtm) REVERT: E 199 MET cc_start: 0.2654 (tpp) cc_final: 0.2278 (tpp) REVERT: E 229 MET cc_start: 0.4249 (mpp) cc_final: 0.3979 (mpp) REVERT: E 249 TYR cc_start: 0.7178 (m-80) cc_final: 0.6789 (m-10) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3061 time to fit residues: 73.2300 Evaluate side-chains 116 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 0.0000 chunk 64 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 400 HIS E 8 GLN E 213 ASN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22532 Z= 0.171 Angle : 0.602 8.501 30750 Z= 0.310 Chirality : 0.043 0.187 3509 Planarity : 0.005 0.050 3799 Dihedral : 14.118 140.259 3482 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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 (0.16), residues: 2670 helix: 0.41 (0.19), residues: 806 sheet: -0.07 (0.20), residues: 637 loop : -2.14 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 56 HIS 0.006 0.001 HIS H 63 PHE 0.013 0.001 PHE A 148 TYR 0.013 0.001 TYR E 249 ARG 0.003 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.806 Fit side-chains revert: symmetry clash REVERT: A 772 MET cc_start: 0.8246 (tpp) cc_final: 0.7823 (mmt) REVERT: A 937 MET cc_start: 0.7020 (mmm) cc_final: 0.6771 (mmm) REVERT: E 68 MET cc_start: 0.5165 (ptt) cc_final: 0.4099 (ptt) REVERT: E 229 MET cc_start: 0.4405 (mpp) cc_final: 0.4075 (mpp) REVERT: H 67 MET cc_start: 0.1754 (tpp) cc_final: 0.1222 (ttt) REVERT: H 180 MET cc_start: 0.0045 (ttm) cc_final: -0.0366 (ttm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3262 time to fit residues: 83.2998 Evaluate side-chains 120 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 220 optimal weight: 0.0170 chunk 146 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22532 Z= 0.152 Angle : 0.590 9.114 30750 Z= 0.301 Chirality : 0.043 0.181 3509 Planarity : 0.004 0.053 3799 Dihedral : 13.874 140.852 3482 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2670 helix: 0.80 (0.19), residues: 792 sheet: 0.04 (0.20), residues: 649 loop : -1.94 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 274 HIS 0.005 0.001 HIS A1021 PHE 0.012 0.001 PHE A 148 TYR 0.017 0.001 TYR E 249 ARG 0.003 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.337 Fit side-chains REVERT: A 198 MET cc_start: 0.6661 (pmm) cc_final: 0.6257 (pmm) REVERT: A 772 MET cc_start: 0.8214 (tpp) cc_final: 0.7999 (mmt) REVERT: A 937 MET cc_start: 0.6942 (mmm) cc_final: 0.6661 (mmm) REVERT: E 229 MET cc_start: 0.4659 (mpp) cc_final: 0.4301 (mpp) REVERT: H 67 MET cc_start: 0.1476 (tpp) cc_final: 0.0982 (ttt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3183 time to fit residues: 79.9625 Evaluate side-chains 119 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22532 Z= 0.240 Angle : 0.642 10.432 30750 Z= 0.327 Chirality : 0.044 0.238 3509 Planarity : 0.005 0.049 3799 Dihedral : 14.029 138.950 3482 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.00 (0.16), residues: 2670 helix: 0.63 (0.19), residues: 806 sheet: 0.01 (0.20), residues: 632 loop : -1.97 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 56 HIS 0.006 0.001 HIS C 72 PHE 0.016 0.001 PHE A1099 TYR 0.016 0.002 TYR G 133 ARG 0.007 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.651 Fit side-chains revert: symmetry clash REVERT: A 772 MET cc_start: 0.8239 (tpp) cc_final: 0.8008 (mmt) REVERT: A 937 MET cc_start: 0.7063 (mmm) cc_final: 0.6780 (mmm) REVERT: E 199 MET cc_start: 0.2266 (tpp) cc_final: 0.1939 (ttm) REVERT: E 229 MET cc_start: 0.4831 (mpp) cc_final: 0.4427 (mpp) REVERT: H 67 MET cc_start: 0.1710 (tpp) cc_final: 0.1234 (ttt) REVERT: H 180 MET cc_start: -0.0152 (ttm) cc_final: -0.0458 (ttm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.3584 time to fit residues: 85.6243 Evaluate side-chains 118 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 0.3980 chunk 250 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 chunk 230 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22532 Z= 0.290 Angle : 0.702 9.973 30750 Z= 0.357 Chirality : 0.045 0.255 3509 Planarity : 0.005 0.055 3799 Dihedral : 14.276 138.221 3482 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.36 (0.16), residues: 2670 helix: 0.23 (0.18), residues: 821 sheet: -0.21 (0.20), residues: 622 loop : -2.10 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 56 HIS 0.007 0.001 HIS C 72 PHE 0.018 0.002 PHE A1099 TYR 0.017 0.002 TYR A 593 ARG 0.009 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.584 Fit side-chains revert: symmetry clash REVERT: A 580 ASP cc_start: 0.6380 (t0) cc_final: 0.6094 (t0) REVERT: A 612 MET cc_start: 0.7866 (tpp) cc_final: 0.7595 (tpp) REVERT: E 47 LEU cc_start: 0.8447 (tt) cc_final: 0.8204 (tt) REVERT: E 199 MET cc_start: 0.2369 (tpp) cc_final: 0.1921 (ttm) REVERT: E 229 MET cc_start: 0.4892 (mpp) cc_final: 0.4423 (mpp) REVERT: H 67 MET cc_start: 0.1807 (tpp) cc_final: 0.1349 (ttt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3178 time to fit residues: 75.4387 Evaluate side-chains 117 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 1.9990 chunk 257 optimal weight: 0.0870 chunk 157 optimal weight: 0.0010 chunk 122 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22532 Z= 0.230 Angle : 0.648 9.600 30750 Z= 0.330 Chirality : 0.044 0.242 3509 Planarity : 0.005 0.050 3799 Dihedral : 14.138 139.305 3482 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.19 (0.16), residues: 2670 helix: 0.41 (0.19), residues: 816 sheet: -0.12 (0.20), residues: 633 loop : -2.03 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 56 HIS 0.006 0.001 HIS A1021 PHE 0.013 0.001 PHE A1099 TYR 0.015 0.001 TYR G 133 ARG 0.005 0.000 ARG B 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.840 Fit side-chains revert: symmetry clash REVERT: A 580 ASP cc_start: 0.6390 (t0) cc_final: 0.6006 (t0) REVERT: E 47 LEU cc_start: 0.8372 (tt) cc_final: 0.8150 (tt) REVERT: E 199 MET cc_start: 0.2528 (tpp) cc_final: 0.2023 (ttm) REVERT: E 229 MET cc_start: 0.4998 (mpp) cc_final: 0.4606 (mpp) REVERT: F 199 MET cc_start: 0.6151 (tpt) cc_final: 0.5073 (tpt) REVERT: H 67 MET cc_start: 0.1583 (tpp) cc_final: 0.1007 (ttt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3281 time to fit residues: 76.3581 Evaluate side-chains 117 residues out of total 2339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 0.0980 chunk 229 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.068376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.050486 restraints weight = 146694.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050978 restraints weight = 91222.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050941 restraints weight = 60200.385| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22532 Z= 0.214 Angle : 0.632 9.690 30750 Z= 0.321 Chirality : 0.044 0.237 3509 Planarity : 0.005 0.049 3799 Dihedral : 13.991 139.407 3482 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % 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: -1.11 (0.16), residues: 2670 helix: 0.53 (0.19), residues: 814 sheet: -0.18 (0.20), residues: 653 loop : -1.98 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 56 HIS 0.014 0.001 HIS A 160 PHE 0.013 0.001 PHE A1099 TYR 0.014 0.001 TYR G 133 ARG 0.005 0.000 ARG B 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.41 seconds wall clock time: 75 minutes 29.06 seconds (4529.06 seconds total)