Starting phenix.real_space_refine on Sat Feb 17 20:30:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s1m_10080/02_2024/6s1m_10080_neut_updated.pdb" } resolution = 4.27 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 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 PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 97.416 99.127 74.603 1.00 40.62 S ATOM 7175 SG CYS A1015 100.426 97.328 76.337 1.00 40.62 S ATOM 7248 SG CYS A1026 101.047 101.039 75.328 1.00 40.62 S ATOM 7264 SG CYS A1029 100.061 98.862 72.781 1.00 40.62 S ATOM 7616 SG CYS A1071 58.262 80.827 75.866 1.00 40.62 S ATOM 7654 SG CYS A1076 62.825 77.203 74.560 1.00 30.94 S ATOM 7515 SG CYS A1058 62.089 83.415 71.486 1.00 40.62 S ATOM 7541 SG CYS A1061 58.417 78.187 70.743 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: 14.48, per 1000 atoms: 0.73 Number of scatterers: 19726 At special positions: 0 Unit cell: (143.64, 128.52, 166.32, 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: 7.37 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " 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: 63 helices and 24 sheets defined 27.3% alpha, 21.3% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 10.66 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: 4.149A 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: 3.591A 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 656 through 676 removed outlier: 4.732A 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: 4.886A 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: 6.704A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.565A 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: 3.542A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.900A 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: 3.721A 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: 4.145A 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 9 through 19 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.844A pdb=" N CYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.739A pdb=" N HIS E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 removed outlier: 3.973A pdb=" N LYS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 4.663A 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 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.875A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.691A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 221 removed outlier: 3.966A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.821A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.677A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 221 removed outlier: 4.020A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 4.700A 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: 4.541A 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: 5.114A 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: 6.267A pdb=" N LEU A 286 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 7.766A 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: 7.270A 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: 3.913A 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: 6.616A 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: 6.983A 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: 6.415A 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: 3.651A 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: 7.726A pdb=" N LEU B 197 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.764A 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: 7.777A 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: 6.608A 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: 6.443A 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 25 through 30 Processing sheet with id= O, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.713A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 203 through 208 removed outlier: 6.020A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 2 through 6 Processing sheet with id= R, first strand: chain 'F' and resid 25 through 29 removed outlier: 3.747A pdb=" N TRP F 28 " --> pdb=" O MET F 68 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 68 " --> pdb=" O TRP F 28 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 34 through 40 removed outlier: 4.717A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.028A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= V, first strand: chain 'G' and resid 25 through 30 Processing sheet with id= W, first strand: chain 'G' and resid 34 through 40 removed outlier: 4.728A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 203 through 208 removed outlier: 6.036A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1938 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: 9.50 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 7993 1.40 - 1.63: 12017 1.63 - 1.85: 186 1.85 - 2.08: 2 2.08 - 2.31: 12 Bond restraints: 20210 Sorted by residual: bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.609 1.277 0.332 2.00e-02 2.50e+03 2.75e+02 bond pdb=" C2' TTP T 101 " pdb=" C3' TTP T 101 " ideal model delta sigma weight residual 1.524 1.217 0.307 2.00e-02 2.50e+03 2.36e+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 1.304 0.185 2.00e-02 2.50e+03 8.51e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 72.66 - 84.98: 12 84.98 - 97.30: 0 97.30 - 109.63: 3839 109.63 - 121.95: 19485 121.95 - 134.27: 4273 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 111.28 119.43 -8.15 1.09e+00 8.42e-01 5.58e+01 angle pdb=" N ASN G 107 " pdb=" CA ASN G 107 " pdb=" C ASN G 107 " ideal model delta sigma weight residual 109.96 98.94 11.02 1.50e+00 4.44e-01 5.40e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.75 7.61 1.09e+00 8.42e-01 4.88e+01 angle pdb=" N ASN G 200 " pdb=" CA ASN G 200 " pdb=" C ASN G 200 " ideal model delta sigma weight residual 113.41 105.15 8.26 1.22e+00 6.72e-01 4.58e+01 angle pdb=" N ASN E 200 " pdb=" CA ASN E 200 " pdb=" C ASN E 200 " ideal model delta sigma weight residual 113.41 105.21 8.20 1.22e+00 6.72e-01 4.51e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 11311 27.54 - 55.08: 728 55.08 - 82.62: 123 82.62 - 110.16: 10 110.16 - 137.71: 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 301.68 163.98 137.71 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 122.80 137.59 -14.79 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 65.21 114.76 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2613 0.099 - 0.198: 469 0.198 - 0.297: 65 0.297 - 0.397: 2 0.397 - 0.496: 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 6.15e+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 6.03e+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 4.07e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 249 " -0.086 2.00e-02 2.50e+03 4.57e-02 4.18e+01 pdb=" CG TYR G 249 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR G 249 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR G 249 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR G 249 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR G 249 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR G 249 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 249 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 249 " -0.077 2.00e-02 2.50e+03 3.98e-02 3.17e+01 pdb=" CG TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR F 249 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR F 249 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 249 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 249 " -0.074 2.00e-02 2.50e+03 3.85e-02 2.96e+01 pdb=" CG TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR E 249 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 249 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 249 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 249 " -0.054 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 5 1.93 - 2.68: 533 2.68 - 3.42: 24845 3.42 - 4.16: 45875 4.16 - 4.90: 81523 Nonbonded interactions: 152781 Sorted by model distance: nonbonded pdb=" ND2 ASN G 84 " pdb=" OP1 DG P 7 " model vdw 1.193 2.520 nonbonded pdb=" CD2 LEU A 995 " pdb=" O ASP F 122 " model vdw 1.806 3.460 nonbonded pdb=" CD1 LEU A 995 " pdb=" CG GLU F 124 " model vdw 1.906 3.860 nonbonded pdb=" O PHE A1005 " pdb=" O GLY F 127 " model vdw 1.927 3.040 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.932 3.860 ... (remaining 152776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 107 or resid 109 through 185 or resid 191 or res \ id 194 through 255)) selection = (chain 'F' and (resid 1 through 191 or resid 194 through 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 185 or resid 193 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 10.400 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 74.510 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 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 : 0.010 0.332 20210 Z= 0.609 Angle : 1.222 11.420 27609 Z= 0.729 Chirality : 0.077 0.496 3152 Planarity : 0.008 0.075 3387 Dihedral : 17.826 137.706 7672 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.22 % Favored : 91.93 % Rotamer: Outliers : 1.46 % Allowed : 7.09 % Favored : 91.45 % 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: -3.67 (0.14), residues: 2370 helix: -2.50 (0.16), residues: 671 sheet: -1.14 (0.19), residues: 615 loop : -3.18 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 344 HIS 0.010 0.002 HIS C 99 PHE 0.042 0.005 PHE E 207 TYR 0.086 0.007 TYR G 249 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 750 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 720 time to evaluate : 2.347 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.4099 (m-80) cc_final: 0.3539 (m-80) REVERT: A 433 ASP cc_start: 0.6570 (m-30) cc_final: 0.6268 (t0) REVERT: A 479 PHE cc_start: 0.8341 (t80) cc_final: 0.8120 (t80) REVERT: A 719 SER cc_start: 0.7565 (m) cc_final: 0.6608 (t) REVERT: A 865 GLN cc_start: 0.7551 (mt0) cc_final: 0.7263 (tm-30) REVERT: A 903 LEU cc_start: 0.8021 (tp) cc_final: 0.7715 (tp) REVERT: A 944 PHE cc_start: 0.8407 (t80) cc_final: 0.8017 (t80) REVERT: D 79 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: E 116 MET cc_start: 0.4464 (ttp) cc_final: 0.2796 (tmm) REVERT: F 50 LEU cc_start: 0.8423 (tp) cc_final: 0.8120 (tp) REVERT: F 75 MET cc_start: 0.6677 (ttt) cc_final: 0.6291 (ttm) REVERT: F 213 ASN cc_start: 0.6758 (m-40) cc_final: 0.6424 (m-40) outliers start: 30 outliers final: 5 residues processed: 744 average time/residue: 0.3900 time to fit residues: 420.7567 Evaluate side-chains 371 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 365 time to evaluate : 2.366 ------------------------------------------------------------------------------- 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: 3.9990 chunk 182 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 188 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 430 ASN A 558 GLN A 726 GLN A 842 ASN A 865 GLN A1092 GLN B 70 GLN B 104 GLN B 140 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 246 ASN B 435 GLN C 17 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN E 213 ASN F 65 ASN F 153 HIS G 65 ASN G 184 GLN G 213 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20210 Z= 0.228 Angle : 0.737 10.634 27609 Z= 0.377 Chirality : 0.046 0.221 3152 Planarity : 0.006 0.083 3387 Dihedral : 15.230 148.372 3159 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 0.24 % Allowed : 3.45 % Favored : 96.31 % 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: -2.04 (0.16), residues: 2370 helix: -0.80 (0.19), residues: 660 sheet: -0.21 (0.20), residues: 647 loop : -2.48 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 28 HIS 0.009 0.001 HIS F 153 PHE 0.035 0.002 PHE E 215 TYR 0.026 0.002 TYR E 133 ARG 0.008 0.001 ARG A 444 *********************** 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 477 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 472 time to evaluate : 2.302 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.6488 (t80) cc_final: 0.6265 (t80) REVERT: A 433 ASP cc_start: 0.6789 (m-30) cc_final: 0.6536 (t0) REVERT: A 479 PHE cc_start: 0.8423 (t80) cc_final: 0.8142 (t80) REVERT: A 523 LEU cc_start: 0.7711 (tp) cc_final: 0.7474 (tt) REVERT: A 843 LEU cc_start: 0.8291 (tp) cc_final: 0.8058 (tp) REVERT: A 865 GLN cc_start: 0.7885 (mt0) cc_final: 0.7262 (mp10) REVERT: A 944 PHE cc_start: 0.8357 (t80) cc_final: 0.7900 (t80) REVERT: A 1082 ARG cc_start: 0.6809 (ptt180) cc_final: 0.6549 (ptt-90) REVERT: B 366 GLU cc_start: 0.8238 (pt0) cc_final: 0.7748 (pp20) REVERT: C 43 ASP cc_start: 0.6236 (t0) cc_final: 0.5965 (t0) REVERT: C 68 ILE cc_start: 0.7937 (mt) cc_final: 0.7547 (tt) REVERT: E 84 ASN cc_start: 0.5650 (t0) cc_final: 0.5437 (t0) REVERT: E 116 MET cc_start: 0.4844 (ttp) cc_final: 0.3558 (tmm) REVERT: E 139 MET cc_start: 0.4102 (pmm) cc_final: 0.3838 (pmm) REVERT: E 215 PHE cc_start: 0.5752 (m-80) cc_final: 0.5403 (m-80) REVERT: F 81 CYS cc_start: 0.7702 (m) cc_final: 0.7070 (m) REVERT: F 207 PHE cc_start: 0.6234 (m-80) cc_final: 0.5727 (m-10) REVERT: F 227 LEU cc_start: 0.7510 (pp) cc_final: 0.7267 (pp) REVERT: G 44 HIS cc_start: 0.7481 (t70) cc_final: 0.7178 (t70) outliers start: 5 outliers final: 0 residues processed: 477 average time/residue: 0.3389 time to fit residues: 245.6089 Evaluate side-chains 342 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN A 948 HIS ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS A1059 GLN A1066 HIS B 11 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN B 333 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS D 68 GLN E 44 HIS E 153 HIS F 49 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20210 Z= 0.238 Angle : 0.695 10.360 27609 Z= 0.355 Chirality : 0.045 0.223 3152 Planarity : 0.006 0.067 3387 Dihedral : 15.042 151.527 3159 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -1.39 (0.17), residues: 2370 helix: -0.12 (0.21), residues: 660 sheet: 0.20 (0.21), residues: 638 loop : -2.19 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 28 HIS 0.006 0.001 HIS F 153 PHE 0.025 0.002 PHE E 214 TYR 0.035 0.002 TYR A 801 ARG 0.007 0.001 ARG A 990 *********************** 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 423 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 2.232 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: A 99 LEU cc_start: 0.7779 (mt) cc_final: 0.7503 (mt) REVERT: A 353 LEU cc_start: 0.8705 (tp) cc_final: 0.8486 (tt) REVERT: A 433 ASP cc_start: 0.7129 (m-30) cc_final: 0.6927 (t0) REVERT: A 865 GLN cc_start: 0.8053 (mt0) cc_final: 0.7851 (mm-40) REVERT: A 944 PHE cc_start: 0.8586 (t80) cc_final: 0.8282 (t80) REVERT: B 366 GLU cc_start: 0.8531 (pt0) cc_final: 0.7696 (tm-30) REVERT: B 406 ASN cc_start: 0.7659 (p0) cc_final: 0.7405 (p0) REVERT: C 7 LEU cc_start: 0.8971 (mt) cc_final: 0.8675 (mt) REVERT: C 11 ASP cc_start: 0.7921 (m-30) cc_final: 0.6995 (m-30) REVERT: C 38 LYS cc_start: 0.7656 (mttt) cc_final: 0.7267 (mttp) REVERT: C 43 ASP cc_start: 0.6275 (t0) cc_final: 0.5925 (t0) REVERT: C 68 ILE cc_start: 0.8232 (mt) cc_final: 0.7950 (tt) REVERT: D 52 PHE cc_start: 0.7937 (t80) cc_final: 0.7608 (t80) REVERT: D 58 TYR cc_start: 0.7322 (m-80) cc_final: 0.7116 (m-80) REVERT: D 67 LEU cc_start: 0.8612 (pt) cc_final: 0.8324 (pp) REVERT: E 84 ASN cc_start: 0.5650 (t0) cc_final: 0.4900 (t0) REVERT: E 119 MET cc_start: 0.3747 (ptp) cc_final: 0.3414 (mtt) REVERT: E 215 PHE cc_start: 0.5963 (m-80) cc_final: 0.5583 (m-80) REVERT: F 207 PHE cc_start: 0.6538 (m-80) cc_final: 0.6187 (m-10) REVERT: G 249 TYR cc_start: 0.3849 (m-80) cc_final: 0.3433 (m-80) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.3205 time to fit residues: 206.1998 Evaluate side-chains 324 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.284 ------------------------------------------------------------------------------- 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: 10.0000 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN A 948 HIS A 988 HIS ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN B 52 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN C 17 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 153 HIS ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20210 Z= 0.276 Angle : 0.727 9.447 27609 Z= 0.370 Chirality : 0.045 0.183 3152 Planarity : 0.006 0.084 3387 Dihedral : 14.954 140.360 3159 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % 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: -1.20 (0.17), residues: 2370 helix: -0.02 (0.20), residues: 665 sheet: 0.26 (0.21), residues: 623 loop : -1.97 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 28 HIS 0.008 0.001 HIS B 250 PHE 0.023 0.002 PHE A 418 TYR 0.022 0.002 TYR F 239 ARG 0.009 0.001 ARG B 57 *********************** 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 404 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.634 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: A 353 LEU cc_start: 0.8717 (tp) cc_final: 0.8464 (tt) REVERT: B 366 GLU cc_start: 0.8637 (pt0) cc_final: 0.7910 (tm-30) REVERT: B 406 ASN cc_start: 0.8002 (p0) cc_final: 0.7768 (p0) REVERT: C 11 ASP cc_start: 0.8016 (m-30) cc_final: 0.7245 (m-30) REVERT: C 43 ASP cc_start: 0.6549 (t0) cc_final: 0.6279 (t0) REVERT: C 68 ILE cc_start: 0.8422 (mt) cc_final: 0.8220 (tt) REVERT: C 120 ASP cc_start: 0.7743 (m-30) cc_final: 0.7282 (m-30) REVERT: E 215 PHE cc_start: 0.6044 (m-10) cc_final: 0.5555 (m-80) REVERT: F 1 MET cc_start: 0.6346 (mmp) cc_final: 0.6085 (mmp) REVERT: F 211 TYR cc_start: 0.7619 (m-80) cc_final: 0.6970 (m-10) REVERT: G 1 MET cc_start: 0.4642 (tmm) cc_final: 0.4047 (tmm) outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.3112 time to fit residues: 192.2576 Evaluate side-chains 304 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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: 6.9990 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 173 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 198 optimal weight: 0.5980 chunk 161 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 165 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN A 865 GLN A1030 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN G 71 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20210 Z= 0.237 Angle : 0.674 8.439 27609 Z= 0.345 Chirality : 0.044 0.171 3152 Planarity : 0.005 0.072 3387 Dihedral : 14.847 145.484 3159 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.09 (0.17), residues: 2370 helix: 0.04 (0.20), residues: 663 sheet: 0.35 (0.21), residues: 599 loop : -1.84 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 28 HIS 0.006 0.001 HIS C 33 PHE 0.024 0.002 PHE B 455 TYR 0.042 0.002 TYR A 801 ARG 0.006 0.001 ARG A 276 *********************** 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 392 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.394 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 353 LEU cc_start: 0.8705 (tp) cc_final: 0.8467 (tt) REVERT: A 433 ASP cc_start: 0.7826 (m-30) cc_final: 0.7583 (m-30) REVERT: A 449 VAL cc_start: 0.8369 (t) cc_final: 0.8165 (t) REVERT: B 180 ASP cc_start: 0.7180 (t0) cc_final: 0.6760 (t0) REVERT: B 218 LEU cc_start: 0.8163 (pp) cc_final: 0.7583 (tt) REVERT: B 315 MET cc_start: 0.7350 (mtm) cc_final: 0.7147 (mtm) REVERT: B 366 GLU cc_start: 0.8558 (pt0) cc_final: 0.7874 (tm-30) REVERT: C 7 LEU cc_start: 0.9116 (mt) cc_final: 0.8795 (mt) REVERT: C 11 ASP cc_start: 0.8406 (m-30) cc_final: 0.7652 (m-30) REVERT: C 68 ILE cc_start: 0.8633 (mt) cc_final: 0.8345 (tp) REVERT: C 120 ASP cc_start: 0.7654 (m-30) cc_final: 0.7436 (m-30) REVERT: D 46 LEU cc_start: 0.8128 (pt) cc_final: 0.7390 (tp) REVERT: E 84 ASN cc_start: 0.5481 (t0) cc_final: 0.5132 (t0) REVERT: E 116 MET cc_start: 0.5192 (tmm) cc_final: 0.4796 (tmm) REVERT: E 215 PHE cc_start: 0.5982 (m-10) cc_final: 0.5524 (m-80) REVERT: F 45 VAL cc_start: 0.7433 (t) cc_final: 0.7230 (t) REVERT: F 207 PHE cc_start: 0.5839 (m-10) cc_final: 0.5552 (m-10) REVERT: F 211 TYR cc_start: 0.7393 (m-80) cc_final: 0.6999 (m-10) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3209 time to fit residues: 194.0745 Evaluate side-chains 301 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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: 1.9990 chunk 209 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN A 948 HIS B 11 HIS B 128 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN F 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20210 Z= 0.186 Angle : 0.640 8.449 27609 Z= 0.326 Chirality : 0.043 0.175 3152 Planarity : 0.005 0.063 3387 Dihedral : 14.708 145.537 3159 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.91 (0.17), residues: 2370 helix: 0.22 (0.20), residues: 667 sheet: 0.47 (0.22), residues: 591 loop : -1.76 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.011 0.001 HIS A 948 PHE 0.033 0.002 PHE A 135 TYR 0.042 0.002 TYR A 809 ARG 0.010 0.001 ARG E 146 *********************** 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 408 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.147 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 353 LEU cc_start: 0.8696 (tp) cc_final: 0.8484 (tt) REVERT: A 727 MET cc_start: 0.7058 (ttm) cc_final: 0.6841 (mtp) REVERT: A 944 PHE cc_start: 0.8619 (t80) cc_final: 0.8128 (t80) REVERT: B 218 LEU cc_start: 0.8212 (pp) cc_final: 0.7732 (tt) REVERT: B 366 GLU cc_start: 0.8514 (pt0) cc_final: 0.7791 (tm-30) REVERT: C 11 ASP cc_start: 0.8384 (m-30) cc_final: 0.7571 (m-30) REVERT: C 40 MET cc_start: 0.8031 (mtp) cc_final: 0.7239 (mtp) REVERT: C 68 ILE cc_start: 0.8614 (mt) cc_final: 0.8308 (tp) REVERT: D 46 LEU cc_start: 0.8022 (pt) cc_final: 0.7329 (tp) REVERT: E 84 ASN cc_start: 0.5558 (t0) cc_final: 0.5255 (t0) REVERT: E 116 MET cc_start: 0.5164 (tmm) cc_final: 0.4856 (tmm) REVERT: E 215 PHE cc_start: 0.5762 (m-10) cc_final: 0.5408 (m-80) REVERT: F 207 PHE cc_start: 0.5674 (m-10) cc_final: 0.5344 (m-10) REVERT: F 211 TYR cc_start: 0.7485 (m-80) cc_final: 0.7284 (m-10) REVERT: F 244 MET cc_start: 0.7068 (mmp) cc_final: 0.6700 (mmm) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3130 time to fit residues: 195.7582 Evaluate side-chains 310 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN B 400 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN G 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.8648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20210 Z= 0.400 Angle : 0.846 14.005 27609 Z= 0.434 Chirality : 0.049 0.185 3152 Planarity : 0.006 0.102 3387 Dihedral : 15.043 129.082 3159 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -1.50 (0.17), residues: 2370 helix: -0.49 (0.19), residues: 681 sheet: 0.04 (0.21), residues: 594 loop : -1.91 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP A 79 HIS 0.023 0.002 HIS A 948 PHE 0.044 0.003 PHE F 215 TYR 0.045 0.003 TYR A 801 ARG 0.015 0.001 ARG A1086 *********************** 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 356 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 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: A 555 VAL cc_start: 0.7842 (p) cc_final: 0.7618 (p) REVERT: A 944 PHE cc_start: 0.8682 (t80) cc_final: 0.8296 (t80) REVERT: B 218 LEU cc_start: 0.8710 (pp) cc_final: 0.8187 (tt) REVERT: B 388 TYR cc_start: 0.8067 (p90) cc_final: 0.7860 (p90) REVERT: B 406 ASN cc_start: 0.8247 (p0) cc_final: 0.7839 (p0) REVERT: C 68 ILE cc_start: 0.8895 (mt) cc_final: 0.8607 (tt) REVERT: E 84 ASN cc_start: 0.6268 (t0) cc_final: 0.5885 (t0) REVERT: E 116 MET cc_start: 0.5764 (tmm) cc_final: 0.5236 (tmm) REVERT: E 199 MET cc_start: 0.2886 (ptp) cc_final: 0.2190 (ttt) REVERT: E 215 PHE cc_start: 0.5754 (m-10) cc_final: 0.5400 (m-80) REVERT: F 207 PHE cc_start: 0.5918 (m-10) cc_final: 0.5448 (m-10) REVERT: F 211 TYR cc_start: 0.7862 (m-80) cc_final: 0.7523 (m-10) REVERT: G 119 MET cc_start: 0.0498 (ptt) cc_final: 0.0011 (pmm) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.3173 time to fit residues: 173.5806 Evaluate side-chains 277 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 147 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 182 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 246 ASN ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN F 153 HIS F 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.8686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20210 Z= 0.178 Angle : 0.687 11.795 27609 Z= 0.346 Chirality : 0.045 0.189 3152 Planarity : 0.005 0.071 3387 Dihedral : 14.860 141.814 3159 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.22 % 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: -1.01 (0.17), residues: 2370 helix: 0.04 (0.20), residues: 666 sheet: 0.35 (0.21), residues: 591 loop : -1.70 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.012 0.001 HIS A 948 PHE 0.029 0.002 PHE F 214 TYR 0.047 0.002 TYR A 801 ARG 0.004 0.001 ARG E 146 *********************** 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 378 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.446 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: A 255 MET cc_start: 0.6540 (mtm) cc_final: 0.6256 (mtm) REVERT: A 502 ASP cc_start: 0.7985 (p0) cc_final: 0.7718 (p0) REVERT: A 944 PHE cc_start: 0.8727 (t80) cc_final: 0.8325 (t80) REVERT: A 1052 SER cc_start: 0.8932 (m) cc_final: 0.8727 (p) REVERT: B 14 LEU cc_start: 0.7702 (mp) cc_final: 0.7110 (mt) REVERT: B 218 LEU cc_start: 0.8562 (pp) cc_final: 0.8224 (tt) REVERT: C 68 ILE cc_start: 0.8838 (mt) cc_final: 0.8624 (tp) REVERT: C 143 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8101 (tpt90) REVERT: E 84 ASN cc_start: 0.5846 (t0) cc_final: 0.5343 (t0) REVERT: E 116 MET cc_start: 0.4909 (tmm) cc_final: 0.4643 (tmm) REVERT: E 199 MET cc_start: 0.2352 (ptp) cc_final: 0.1787 (ttt) REVERT: E 215 PHE cc_start: 0.5936 (m-10) cc_final: 0.5541 (m-80) REVERT: F 207 PHE cc_start: 0.5596 (m-10) cc_final: 0.4790 (m-10) REVERT: F 211 TYR cc_start: 0.7692 (m-80) cc_final: 0.7485 (m-10) REVERT: G 119 MET cc_start: 0.0942 (ptt) cc_final: 0.0691 (ptt) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.3042 time to fit residues: 177.9077 Evaluate side-chains 294 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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: 6.9990 chunk 203 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 285 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN G 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20210 Z= 0.192 Angle : 0.664 12.060 27609 Z= 0.336 Chirality : 0.044 0.162 3152 Planarity : 0.005 0.062 3387 Dihedral : 14.771 143.709 3159 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % 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: -0.84 (0.17), residues: 2370 helix: 0.25 (0.21), residues: 663 sheet: 0.37 (0.21), residues: 590 loop : -1.59 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 28 HIS 0.005 0.001 HIS A1021 PHE 0.020 0.002 PHE A 479 TYR 0.044 0.002 TYR A 801 ARG 0.004 0.000 ARG B 57 *********************** 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 365 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.760 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 502 ASP cc_start: 0.8052 (p0) cc_final: 0.7685 (p0) REVERT: A 546 LEU cc_start: 0.9053 (mt) cc_final: 0.8817 (mt) REVERT: A 944 PHE cc_start: 0.8748 (t80) cc_final: 0.8337 (t80) REVERT: A 971 GLU cc_start: 0.6942 (tp30) cc_final: 0.6733 (tp30) REVERT: B 14 LEU cc_start: 0.7761 (mp) cc_final: 0.7234 (mt) REVERT: B 218 LEU cc_start: 0.8659 (pp) cc_final: 0.8319 (tt) REVERT: C 143 ARG cc_start: 0.8530 (tpt90) cc_final: 0.8206 (tpt90) REVERT: D 46 LEU cc_start: 0.8355 (pt) cc_final: 0.7350 (tp) REVERT: E 24 ASN cc_start: 0.4067 (p0) cc_final: 0.3481 (p0) REVERT: E 84 ASN cc_start: 0.5756 (t0) cc_final: 0.5281 (t0) REVERT: E 199 MET cc_start: 0.2392 (ptp) cc_final: 0.1811 (ttt) REVERT: E 215 PHE cc_start: 0.5842 (m-10) cc_final: 0.5567 (m-80) REVERT: F 75 MET cc_start: 0.6836 (ptm) cc_final: 0.6114 (ptp) REVERT: G 119 MET cc_start: 0.0641 (ptt) cc_final: 0.0375 (ptt) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.3077 time to fit residues: 173.3337 Evaluate side-chains 298 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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: 6.9990 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 159 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 147 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 151 optimal weight: 0.0170 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.8965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20210 Z= 0.172 Angle : 0.671 10.973 27609 Z= 0.338 Chirality : 0.044 0.270 3152 Planarity : 0.005 0.060 3387 Dihedral : 14.708 145.845 3159 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.76 % 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: -0.69 (0.17), residues: 2370 helix: 0.32 (0.21), residues: 663 sheet: 0.42 (0.21), residues: 609 loop : -1.47 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 265 HIS 0.006 0.001 HIS A1021 PHE 0.039 0.002 PHE F 214 TYR 0.045 0.002 TYR A 801 ARG 0.009 0.000 ARG F 210 ********************** 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 367 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 2.288 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: A 451 MET cc_start: 0.6514 (mmm) cc_final: 0.6073 (mmm) REVERT: A 502 ASP cc_start: 0.8022 (p0) cc_final: 0.7644 (p0) REVERT: A 546 LEU cc_start: 0.9037 (mt) cc_final: 0.8773 (mt) REVERT: A 944 PHE cc_start: 0.8722 (t80) cc_final: 0.8127 (t80) REVERT: B 218 LEU cc_start: 0.8660 (pp) cc_final: 0.8383 (tt) REVERT: C 143 ARG cc_start: 0.8484 (tpt90) cc_final: 0.8204 (tpt90) REVERT: D 46 LEU cc_start: 0.8217 (pt) cc_final: 0.7283 (tp) REVERT: E 24 ASN cc_start: 0.4248 (p0) cc_final: 0.3572 (p0) REVERT: E 84 ASN cc_start: 0.5718 (t0) cc_final: 0.5246 (t0) REVERT: E 116 MET cc_start: 0.4646 (tmm) cc_final: 0.2941 (tmm) REVERT: E 199 MET cc_start: 0.2256 (ptp) cc_final: 0.1786 (ttt) REVERT: E 215 PHE cc_start: 0.5799 (m-10) cc_final: 0.5501 (m-80) REVERT: F 75 MET cc_start: 0.6795 (ptm) cc_final: 0.6344 (ptp) REVERT: G 40 MET cc_start: 0.3162 (mmt) cc_final: 0.2628 (mmp) REVERT: G 119 MET cc_start: 0.0648 (ptt) cc_final: 0.0439 (ptt) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.3095 time to fit residues: 176.1697 Evaluate side-chains 301 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 128 ASN G 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.104597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080414 restraints weight = 73600.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082749 restraints weight = 42309.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.084324 restraints weight = 28168.752| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.9188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20210 Z= 0.240 Angle : 0.691 12.418 27609 Z= 0.351 Chirality : 0.045 0.251 3152 Planarity : 0.005 0.063 3387 Dihedral : 14.715 142.656 3159 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.81 % 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: -0.77 (0.17), residues: 2370 helix: 0.27 (0.21), residues: 668 sheet: 0.28 (0.21), residues: 625 loop : -1.49 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 79 HIS 0.010 0.001 HIS B 250 PHE 0.044 0.002 PHE F 214 TYR 0.042 0.002 TYR A 801 ARG 0.008 0.001 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.32 seconds wall clock time: 87 minutes 50.68 seconds (5270.68 seconds total)