Starting phenix.real_space_refine on Thu Jun 19 02:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.map" model { file = "/net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ash_43814/06_2025/9ash_43814.cif" } resolution = 2.58 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= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 66 5.49 5 Mg 3 5.21 5 S 53 5.16 5 C 13950 2.51 5 N 3799 2.21 5 O 4438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6078 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2401 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 10, 'TRANS': 286} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1620 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 792 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna2p': 19, 'rna3p': 17} Chain: "D" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain: "E" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 467 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 20} Chain: "C" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 134} Chain: "J" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2506 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'ATP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, None: 1} Not linked: pdbres="ATP P 1 " pdbres=" A P 2 " Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' MG': 3, 'ATP': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 20.05, per 1000 atoms: 0.90 Number of scatterers: 22309 At special positions: 0 Unit cell: (95.586, 122.436, 207.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 66 15.00 Mg 3 11.99 O 4438 8.00 N 3799 7.00 C 13950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 405 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.02 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 7.07 Conformation dependent library (CDL) restraints added in 4.1 seconds 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 31 sheets defined 44.6% alpha, 14.8% beta 15 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.530A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 21 removed outlier: 4.120A pdb=" N ILE A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.692A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.687A pdb=" N VAL A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.635A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 202 through 225 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 271 through 295 removed outlier: 4.449A pdb=" N ALA A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 317 through 339 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 364 through 381 removed outlier: 4.326A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.670A pdb=" N GLN A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.225A pdb=" N LEU A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 538 through 564 removed outlier: 4.030A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.020A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 637 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.670A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 removed outlier: 3.786A pdb=" N ALA A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 739 through 754 Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.564A pdb=" N GLU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 4.183A pdb=" N TYR B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.663A pdb=" N LEU B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 45 through 63 Processing helix chain 'F' and resid 74 through 82 removed outlier: 3.945A pdb=" N LEU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 removed outlier: 3.630A pdb=" N THR F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.500A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 63 removed outlier: 3.846A pdb=" N ASN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.654A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.635A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 174 Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 174 Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.534A pdb=" N LEU G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.517A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 158 through 174 removed outlier: 3.628A pdb=" N PHE I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.535A pdb=" N LEU I 208 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'D' and resid 57 through 73 removed outlier: 3.798A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 147 removed outlier: 3.556A pdb=" N PHE D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 57 through 73 removed outlier: 4.257A pdb=" N ASN E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.814A pdb=" N GLU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 147 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 57 through 73 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.681A pdb=" N ASP C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 removed outlier: 3.854A pdb=" N PHE C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 144 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 54 through 60 Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.605A pdb=" N VAL J 73 " --> pdb=" O TYR J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 140 removed outlier: 4.126A pdb=" N ALA J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 3.751A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 155' Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 226 Processing helix chain 'J' and resid 228 through 237 Processing helix chain 'J' and resid 276 through 280 Processing helix chain 'J' and resid 287 through 303 removed outlier: 3.650A pdb=" N LEU J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 305 removed outlier: 5.981A pdb=" N ILE A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 313 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 305 removed outlier: 5.981A pdb=" N ILE A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 313 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.284A pdb=" N ILE A 417 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.629A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 473 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 583 removed outlier: 4.148A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.531A pdb=" N THR B 153 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE B 8 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.705A pdb=" N LYS B 58 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 160 " --> pdb=" O LYS B 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB3, first strand: chain 'B' and resid 272 through 277 removed outlier: 6.317A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.866A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 184 removed outlier: 7.669A pdb=" N GLY F 184 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE G 96 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN G 97 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU G 147 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 188 through 197 removed outlier: 5.626A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 7 " --> pdb=" O PHE H 146 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU H 147 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN H 97 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY G 184 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'H' and resid 115 through 124 removed outlier: 3.564A pdb=" N VAL H 129 " --> pdb=" O ASN H 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 183 through 184 removed outlier: 4.401A pdb=" N ASN I 97 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU I 147 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 7 " --> pdb=" O PHE I 146 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR I 8 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN I 192 " --> pdb=" O THR I 8 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL I 10 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE I 190 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC5, first strand: chain 'G' and resid 115 through 123 Processing sheet with id=AC6, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'I' and resid 115 through 123 Processing sheet with id=AC8, first strand: chain 'I' and resid 183 through 184 removed outlier: 5.313A pdb=" N THR J 200 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AD1, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.954A pdb=" N PHE D 42 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 18 through 22 removed outlier: 4.073A pdb=" N GLY J 20 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP J 112 " --> pdb=" O TYR J 187 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLU J 189 " --> pdb=" O ASP J 112 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN J 114 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU J 191 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N PHE J 116 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 28 through 31 Processing sheet with id=AD4, first strand: chain 'J' and resid 314 through 315 removed outlier: 3.571A pdb=" N LEU J 340 " --> pdb=" O ASP J 315 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 13.18 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7193 1.35 - 1.49: 5952 1.49 - 1.63: 9557 1.63 - 1.76: 10 1.76 - 1.90: 99 Bond restraints: 22811 Sorted by residual: bond pdb=" C1' ATP P 1 " pdb=" C2' ATP P 1 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.46e+02 bond pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.45e+02 bond pdb=" C3' ATP P 1 " pdb=" C4' ATP P 1 " ideal model delta sigma weight residual 1.526 1.340 0.186 1.10e-02 8.26e+03 2.87e+02 bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.341 0.185 1.10e-02 8.26e+03 2.82e+02 bond pdb=" C1' ATP P 1 " pdb=" O4' ATP P 1 " ideal model delta sigma weight residual 1.416 1.582 -0.166 1.30e-02 5.92e+03 1.64e+02 ... (remaining 22806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 30921 3.95 - 7.90: 85 7.90 - 11.85: 5 11.85 - 15.80: 2 15.80 - 19.75: 2 Bond angle restraints: 31015 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.25 16.62 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PB ATP P 1 " pdb=" O3B ATP P 1 " pdb=" PG ATP P 1 " ideal model delta sigma weight residual 139.87 124.93 14.94 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 124.23 12.60 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP P 1 " pdb=" O3A ATP P 1 " pdb=" PB ATP P 1 " ideal model delta sigma weight residual 136.83 125.23 11.60 1.00e+00 1.00e+00 1.35e+02 angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.15 -19.75 2.30e+00 1.89e-01 7.37e+01 ... (remaining 31010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 13449 34.73 - 69.45: 385 69.45 - 104.18: 52 104.18 - 138.91: 4 138.91 - 173.63: 2 Dihedral angle restraints: 13892 sinusoidal: 6276 harmonic: 7616 Sorted by residual: dihedral pdb=" O4' U T 8 " pdb=" C1' U T 8 " pdb=" N1 U T 8 " pdb=" C2 U T 8 " ideal model delta sinusoidal sigma weight residual 200.00 61.93 138.07 1 1.50e+01 4.44e-03 7.44e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual 93.00 19.96 73.04 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual -86.00 -151.61 65.61 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 13889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3051 0.062 - 0.125: 418 0.125 - 0.187: 29 0.187 - 0.249: 5 0.249 - 0.311: 5 Chirality restraints: 3508 Sorted by residual: chirality pdb=" C1' G R 21 " pdb=" O4' G R 21 " pdb=" C2' G R 21 " pdb=" N9 G R 21 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1' C R 15 " pdb=" O4' C R 15 " pdb=" C2' C R 15 " pdb=" N1 C R 15 " both_signs ideal model delta sigma weight residual False 2.45 2.16 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3505 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C R 15 " -0.045 2.00e-02 2.50e+03 2.39e-02 1.29e+01 pdb=" N1 C R 15 " 0.053 2.00e-02 2.50e+03 pdb=" C2 C R 15 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C R 15 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C R 15 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C R 15 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C R 15 " -0.015 2.00e-02 2.50e+03 pdb=" C5 C R 15 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C R 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 21 " -0.048 2.00e-02 2.50e+03 2.05e-02 1.27e+01 pdb=" N9 G R 21 " 0.049 2.00e-02 2.50e+03 pdb=" C8 G R 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G R 21 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G R 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G R 21 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G R 21 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G R 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G R 21 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G R 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 21 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G R 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 19 " 0.032 2.00e-02 2.50e+03 1.65e-02 6.14e+00 pdb=" N1 C R 19 " -0.035 2.00e-02 2.50e+03 pdb=" C2 C R 19 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C R 19 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C R 19 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C R 19 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C R 19 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C R 19 " -0.004 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 193 2.55 - 3.14: 17507 3.14 - 3.73: 36037 3.73 - 4.31: 53572 4.31 - 4.90: 87544 Nonbonded interactions: 194853 Sorted by model distance: nonbonded pdb=" OD1 ASP A 520 " pdb="MG MG A 803 " model vdw 1.963 2.170 nonbonded pdb=" O VAL A 521 " pdb="MG MG A 803 " model vdw 1.998 2.170 nonbonded pdb=" OD1 ASP A 577 " pdb="MG MG A 802 " model vdw 2.010 2.170 nonbonded pdb=" O2G ATP P 1 " pdb="MG MG A 803 " model vdw 2.020 2.170 nonbonded pdb=" O1B ATP P 1 " pdb="MG MG A 803 " model vdw 2.024 2.170 ... (remaining 194848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 12 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 149)) selection = (chain 'D' and (resid 12 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 149)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 652.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 74.160 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:29.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 759.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.005 0.223 22816 Z= 0.363 Angle : 0.650 19.750 31023 Z= 0.393 Chirality : 0.043 0.311 3508 Planarity : 0.003 0.032 3755 Dihedral : 16.628 173.634 8980 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.64 (0.16), residues: 2594 helix: 0.82 (0.16), residues: 1096 sheet: -0.43 (0.25), residues: 388 loop : -1.71 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.004 0.001 HIS A 363 PHE 0.018 0.001 PHE A 553 TYR 0.013 0.001 TYR B 186 ARG 0.007 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.16126 ( 1013) hydrogen bonds : angle 7.13552 ( 2929) SS BOND : bond 0.01033 ( 4) SS BOND : angle 7.59364 ( 8) covalent geometry : bond 0.00518 (22811) covalent geometry : angle 0.63859 (31015) Misc. bond : bond 0.04155 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 3.291 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8544 (tpp) cc_final: 0.8222 (tpp) REVERT: E 137 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 134 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8409 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 1.7622 time to fit residues: 705.3797 Evaluate side-chains 266 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 176 ASN A 251 ASN A 381 ASN A 435 ASN A 460 GLN A 484 ASN A 526 GLN A 530 ASN A 555 ASN A 680 ASN A 709 ASN B 55 ASN B 134 HIS B 267 ASN F 62 ASN F 74 GLN F 131 ASN H 124 ASN H 180 HIS H 201 ASN G 16 HIS I 72 ASN I 134 GLN I 206 ASN D 50 GLN E 22 ASN E 25 ASN E 65 ASN C 39 HIS C 73 ASN C 75 ASN C 82 ASN C 123 GLN J 38 HIS J 42 HIS J 65 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN J 301 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133048 restraints weight = 23746.209| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.84 r_work: 0.3342 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22816 Z= 0.190 Angle : 0.630 20.144 31023 Z= 0.339 Chirality : 0.045 0.344 3508 Planarity : 0.004 0.040 3755 Dihedral : 14.983 169.460 3832 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 1.59 % Allowed : 10.22 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.56 (0.16), residues: 2594 helix: 0.90 (0.16), residues: 1110 sheet: -0.43 (0.26), residues: 389 loop : -1.70 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 334 HIS 0.006 0.001 HIS A 363 PHE 0.028 0.002 PHE E 26 TYR 0.023 0.002 TYR A 458 ARG 0.008 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 1013) hydrogen bonds : angle 5.49663 ( 2929) SS BOND : bond 0.01363 ( 4) SS BOND : angle 8.00363 ( 8) covalent geometry : bond 0.00432 (22811) covalent geometry : angle 0.61707 (31015) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 2.554 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: A 243 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 249 MET cc_start: 0.8621 (tpp) cc_final: 0.8291 (tpp) REVERT: A 488 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.7697 (ttp-110) REVERT: B 200 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7441 (mt-10) REVERT: F 74 GLN cc_start: 0.7717 (tp40) cc_final: 0.7440 (tp-100) REVERT: H 154 ASP cc_start: 0.7644 (t0) cc_final: 0.7412 (t0) REVERT: H 180 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8526 (m170) REVERT: G 159 GLU cc_start: 0.7805 (mm-30) cc_final: 0.6886 (pm20) REVERT: G 160 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.6970 (mtpt) REVERT: I 174 PHE cc_start: 0.7617 (m-80) cc_final: 0.6910 (m-80) REVERT: E 73 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6781 (m110) REVERT: E 137 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7345 (mt-10) REVERT: C 124 ARG cc_start: 0.7480 (mtt90) cc_final: 0.6709 (mtp-110) REVERT: J 36 VAL cc_start: 0.4370 (t) cc_final: 0.3974 (p) REVERT: J 51 GLU cc_start: 0.4775 (mm-30) cc_final: 0.3723 (mm-30) outliers start: 36 outliers final: 17 residues processed: 308 average time/residue: 1.3249 time to fit residues: 466.6375 Evaluate side-chains 280 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 138 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 180 GLN F 62 ASN H 180 HIS H 201 ASN G 111 ASN I 134 GLN I 180 HIS E 73 ASN C 75 ASN C 82 ASN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.178341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137894 restraints weight = 23460.112| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.82 r_work: 0.3378 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 22816 Z= 0.141 Angle : 0.572 19.485 31023 Z= 0.309 Chirality : 0.042 0.338 3508 Planarity : 0.003 0.047 3755 Dihedral : 14.870 169.362 3832 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 1.77 % Allowed : 12.30 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.43 (0.16), residues: 2594 helix: 1.06 (0.16), residues: 1110 sheet: -0.32 (0.26), residues: 380 loop : -1.70 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.011 0.001 HIS H 180 PHE 0.018 0.001 PHE E 129 TYR 0.013 0.001 TYR E 135 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 1013) hydrogen bonds : angle 5.18383 ( 2929) SS BOND : bond 0.01237 ( 4) SS BOND : angle 7.68926 ( 8) covalent geometry : bond 0.00308 (22811) covalent geometry : angle 0.55821 (31015) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 3.209 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7043 (pp20) REVERT: A 171 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: A 243 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7578 (t0) REVERT: A 249 MET cc_start: 0.8579 (tpp) cc_final: 0.8315 (tpp) REVERT: A 488 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.7714 (ttp-110) REVERT: B 135 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8010 (t0) REVERT: B 200 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7475 (mt-10) REVERT: F 74 GLN cc_start: 0.7719 (tp40) cc_final: 0.7485 (tp40) REVERT: H 154 ASP cc_start: 0.7710 (t0) cc_final: 0.7443 (t0) REVERT: G 159 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7047 (pm20) REVERT: G 160 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7089 (mtpt) REVERT: I 174 PHE cc_start: 0.7621 (m-80) cc_final: 0.6909 (m-80) REVERT: E 73 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6928 (m110) REVERT: J 36 VAL cc_start: 0.4471 (t) cc_final: 0.4061 (p) outliers start: 40 outliers final: 12 residues processed: 318 average time/residue: 1.4319 time to fit residues: 521.7010 Evaluate side-chains 292 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN F 62 ASN H 180 HIS G 111 ASN I 134 GLN C 25 ASN C 38 ASN C 44 ASN C 75 ASN C 82 ASN J 282 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135774 restraints weight = 23572.520| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.83 r_work: 0.3346 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 22816 Z= 0.181 Angle : 0.600 19.811 31023 Z= 0.323 Chirality : 0.044 0.351 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.872 169.548 3832 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 2.48 % Allowed : 14.29 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.45 (0.16), residues: 2594 helix: 1.03 (0.16), residues: 1112 sheet: -0.30 (0.26), residues: 368 loop : -1.69 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.010 0.001 HIS H 180 PHE 0.021 0.002 PHE A 553 TYR 0.022 0.002 TYR A 458 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1013) hydrogen bonds : angle 5.17090 ( 2929) SS BOND : bond 0.01385 ( 4) SS BOND : angle 7.94667 ( 8) covalent geometry : bond 0.00409 (22811) covalent geometry : angle 0.58659 (31015) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 273 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: A 41 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7072 (pp20) REVERT: A 171 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: A 243 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7636 (t0) REVERT: A 249 MET cc_start: 0.8571 (tpp) cc_final: 0.8303 (tpp) REVERT: B 135 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8080 (t0) REVERT: B 200 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7547 (mt-10) REVERT: B 266 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: H 116 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: G 159 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7168 (pm20) REVERT: E 73 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6968 (m110) REVERT: C 101 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: J 3 LYS cc_start: 0.7643 (mttm) cc_final: 0.7045 (mtpt) REVERT: J 36 VAL cc_start: 0.4529 (t) cc_final: 0.4117 (p) REVERT: J 67 ASP cc_start: 0.4477 (m-30) cc_final: 0.4066 (m-30) REVERT: J 81 MET cc_start: 0.4523 (mpp) cc_final: 0.4090 (mpm) REVERT: J 162 GLU cc_start: 0.5662 (mm-30) cc_final: 0.5343 (mm-30) outliers start: 56 outliers final: 22 residues processed: 306 average time/residue: 1.3167 time to fit residues: 463.9337 Evaluate side-chains 294 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 223 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 680 ASN H 180 HIS G 111 ASN I 134 GLN C 75 ASN C 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136091 restraints weight = 23490.794| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.85 r_work: 0.3350 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22816 Z= 0.166 Angle : 0.587 19.676 31023 Z= 0.316 Chirality : 0.043 0.353 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.852 169.379 3832 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 2.70 % Allowed : 15.44 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.42 (0.16), residues: 2594 helix: 1.06 (0.16), residues: 1111 sheet: -0.38 (0.26), residues: 375 loop : -1.66 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.008 0.001 HIS H 180 PHE 0.023 0.002 PHE E 129 TYR 0.016 0.001 TYR E 135 ARG 0.005 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1013) hydrogen bonds : angle 5.10339 ( 2929) SS BOND : bond 0.01333 ( 4) SS BOND : angle 7.88347 ( 8) covalent geometry : bond 0.00372 (22811) covalent geometry : angle 0.57370 (31015) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7077 (pp20) REVERT: A 171 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: A 243 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 249 MET cc_start: 0.8578 (tpp) cc_final: 0.8269 (tpp) REVERT: A 488 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.7868 (ttp-110) REVERT: B 135 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8088 (t0) REVERT: B 200 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7431 (mt-10) REVERT: B 260 LYS cc_start: 0.8558 (mttm) cc_final: 0.8316 (mtpp) REVERT: B 266 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: F 116 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: H 116 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: G 159 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7157 (pm20) REVERT: I 122 THR cc_start: 0.5911 (OUTLIER) cc_final: 0.5687 (t) REVERT: E 73 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.6987 (m110) REVERT: J 3 LYS cc_start: 0.7759 (mttm) cc_final: 0.7143 (mtpt) REVERT: J 67 ASP cc_start: 0.4583 (m-30) cc_final: 0.4167 (m-30) outliers start: 61 outliers final: 25 residues processed: 322 average time/residue: 1.3032 time to fit residues: 482.7545 Evaluate side-chains 299 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain J residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 163 optimal weight: 0.0570 chunk 176 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 136 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN H 180 HIS C 38 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.175960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135242 restraints weight = 23437.922| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.81 r_work: 0.3337 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22816 Z= 0.184 Angle : 0.605 19.692 31023 Z= 0.325 Chirality : 0.044 0.359 3508 Planarity : 0.004 0.046 3755 Dihedral : 14.865 169.462 3832 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 3.05 % Allowed : 15.66 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.46 (0.16), residues: 2594 helix: 1.03 (0.16), residues: 1112 sheet: -0.34 (0.26), residues: 386 loop : -1.72 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.010 0.001 HIS H 180 PHE 0.022 0.002 PHE E 129 TYR 0.024 0.002 TYR A 458 ARG 0.005 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 1013) hydrogen bonds : angle 5.12444 ( 2929) SS BOND : bond 0.01411 ( 4) SS BOND : angle 8.01530 ( 8) covalent geometry : bond 0.00417 (22811) covalent geometry : angle 0.59142 (31015) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 2.636 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: A 243 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 249 MET cc_start: 0.8589 (tpp) cc_final: 0.8308 (tpp) REVERT: B 135 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 200 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 260 LYS cc_start: 0.8599 (mttm) cc_final: 0.8354 (mtpp) REVERT: B 266 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: B 273 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8565 (mm) REVERT: F 1 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6671 (ptp) REVERT: F 116 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: H 116 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: I 122 THR cc_start: 0.5872 (OUTLIER) cc_final: 0.5646 (t) REVERT: E 73 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.6953 (m110) REVERT: C 101 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: J 3 LYS cc_start: 0.7741 (mttm) cc_final: 0.7098 (mtpt) REVERT: J 36 VAL cc_start: 0.4500 (t) cc_final: 0.4034 (p) REVERT: J 67 ASP cc_start: 0.4511 (m-30) cc_final: 0.4092 (m-30) REVERT: J 81 MET cc_start: 0.4505 (mpp) cc_final: 0.4048 (mpm) REVERT: J 162 GLU cc_start: 0.5538 (mm-30) cc_final: 0.5232 (mm-30) outliers start: 69 outliers final: 31 residues processed: 319 average time/residue: 1.3793 time to fit residues: 505.1955 Evaluate side-chains 308 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 52 optimal weight: 0.2980 chunk 221 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN H 180 HIS I 134 GLN E 73 ASN C 38 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138508 restraints weight = 23558.313| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.81 r_work: 0.3389 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22816 Z= 0.127 Angle : 0.559 19.093 31023 Z= 0.302 Chirality : 0.042 0.341 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.788 169.010 3832 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 2.39 % Allowed : 17.17 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.28 (0.16), residues: 2594 helix: 1.22 (0.16), residues: 1107 sheet: -0.31 (0.26), residues: 392 loop : -1.63 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 228 HIS 0.011 0.001 HIS H 180 PHE 0.021 0.001 PHE E 129 TYR 0.018 0.001 TYR E 135 ARG 0.005 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1013) hydrogen bonds : angle 4.94214 ( 2929) SS BOND : bond 0.01182 ( 4) SS BOND : angle 7.62876 ( 8) covalent geometry : bond 0.00272 (22811) covalent geometry : angle 0.54555 (31015) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 2.894 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7029 (pp20) REVERT: A 171 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 243 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7590 (t0) REVERT: A 249 MET cc_start: 0.8538 (tpp) cc_final: 0.8230 (tpp) REVERT: B 135 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8082 (t0) REVERT: B 200 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 266 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: B 273 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8387 (mm) REVERT: F 1 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6647 (ptp) REVERT: H 116 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: G 159 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7044 (pm20) REVERT: I 122 THR cc_start: 0.5928 (OUTLIER) cc_final: 0.5714 (t) REVERT: E 73 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.6996 (m110) REVERT: C 75 ASN cc_start: 0.7533 (p0) cc_final: 0.7104 (t0) REVERT: C 101 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: J 3 LYS cc_start: 0.7751 (mttm) cc_final: 0.7048 (mtpt) REVERT: J 36 VAL cc_start: 0.4501 (t) cc_final: 0.4113 (p) REVERT: J 67 ASP cc_start: 0.4551 (m-30) cc_final: 0.4150 (m-30) REVERT: J 162 GLU cc_start: 0.5720 (mm-30) cc_final: 0.5426 (mm-30) outliers start: 54 outliers final: 22 residues processed: 333 average time/residue: 1.3332 time to fit residues: 512.6449 Evaluate side-chains 310 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.0370 chunk 197 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 238 optimal weight: 0.0870 chunk 226 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN A 646 GLN A 680 ASN A 706 GLN H 180 HIS G 180 HIS I 192 ASN E 69 ASN E 73 ASN C 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.180873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140847 restraints weight = 23383.766| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.71 r_work: 0.3431 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 22816 Z= 0.108 Angle : 0.538 18.742 31023 Z= 0.292 Chirality : 0.041 0.318 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.694 168.878 3832 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 2.04 % Allowed : 17.74 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.14 (0.17), residues: 2594 helix: 1.37 (0.16), residues: 1107 sheet: -0.33 (0.26), residues: 388 loop : -1.57 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 228 HIS 0.013 0.001 HIS H 180 PHE 0.021 0.001 PHE E 129 TYR 0.022 0.001 TYR A 458 ARG 0.005 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 1013) hydrogen bonds : angle 4.78895 ( 2929) SS BOND : bond 0.01067 ( 4) SS BOND : angle 7.42933 ( 8) covalent geometry : bond 0.00223 (22811) covalent geometry : angle 0.52436 (31015) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 2.456 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6962 (pp20) REVERT: A 86 MET cc_start: 0.4901 (mtm) cc_final: 0.4231 (pmm) REVERT: A 243 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7476 (t0) REVERT: A 249 MET cc_start: 0.8514 (tpp) cc_final: 0.8207 (tpp) REVERT: A 430 ASP cc_start: 0.7039 (m-30) cc_final: 0.6703 (m-30) REVERT: A 686 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5889 (mt-10) REVERT: B 135 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8091 (t0) REVERT: B 200 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 266 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: B 273 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8172 (mm) REVERT: F 1 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6668 (ptp) REVERT: F 204 LYS cc_start: 0.7867 (mttp) cc_final: 0.7425 (tppt) REVERT: H 116 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: G 159 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6962 (pm20) REVERT: G 160 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7079 (mtpt) REVERT: I 122 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5718 (t) REVERT: E 73 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6848 (m110) REVERT: C 75 ASN cc_start: 0.7515 (p0) cc_final: 0.7162 (t0) REVERT: C 101 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: J 3 LYS cc_start: 0.7782 (mttm) cc_final: 0.7110 (mtpt) REVERT: J 36 VAL cc_start: 0.4571 (t) cc_final: 0.4201 (p) REVERT: J 67 ASP cc_start: 0.4544 (m-30) cc_final: 0.4304 (m-30) REVERT: J 162 GLU cc_start: 0.5785 (mm-30) cc_final: 0.5477 (mm-30) outliers start: 46 outliers final: 14 residues processed: 334 average time/residue: 1.2953 time to fit residues: 497.6320 Evaluate side-chains 302 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 169 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN H 180 HIS ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN C 38 ASN C 82 ASN C 122 ASN ** J 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137186 restraints weight = 23457.708| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.91 r_work: 0.3347 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 22816 Z= 0.167 Angle : 0.593 19.352 31023 Z= 0.318 Chirality : 0.043 0.343 3508 Planarity : 0.004 0.044 3755 Dihedral : 14.777 169.304 3832 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 2.17 % Allowed : 17.61 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.24 (0.16), residues: 2594 helix: 1.26 (0.16), residues: 1105 sheet: -0.32 (0.26), residues: 376 loop : -1.60 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 228 HIS 0.009 0.001 HIS H 180 PHE 0.024 0.002 PHE E 26 TYR 0.014 0.001 TYR G 176 ARG 0.007 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1013) hydrogen bonds : angle 4.94909 ( 2929) SS BOND : bond 0.01359 ( 4) SS BOND : angle 7.84721 ( 8) covalent geometry : bond 0.00377 (22811) covalent geometry : angle 0.57993 (31015) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 3.026 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7071 (pp20) REVERT: A 86 MET cc_start: 0.4988 (mtm) cc_final: 0.4533 (ptt) REVERT: A 171 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: A 243 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: A 249 MET cc_start: 0.8563 (tpp) cc_final: 0.8326 (tpp) REVERT: A 430 ASP cc_start: 0.6982 (m-30) cc_final: 0.6649 (m-30) REVERT: A 722 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: B 135 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8161 (t0) REVERT: B 200 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7378 (mt-10) REVERT: B 273 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8389 (mm) REVERT: F 1 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6673 (ptp) REVERT: H 116 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8410 (pt0) REVERT: G 159 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7052 (pm20) REVERT: I 122 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5685 (t) REVERT: E 73 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6989 (m110) REVERT: C 75 ASN cc_start: 0.7559 (p0) cc_final: 0.7166 (t0) REVERT: C 101 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: J 3 LYS cc_start: 0.7807 (mttm) cc_final: 0.7138 (mtpt) REVERT: J 36 VAL cc_start: 0.4399 (t) cc_final: 0.4027 (p) REVERT: J 67 ASP cc_start: 0.4504 (m-30) cc_final: 0.4117 (m-30) REVERT: J 81 MET cc_start: 0.4258 (mpp) cc_final: 0.3767 (mpm) REVERT: J 162 GLU cc_start: 0.5728 (mm-30) cc_final: 0.5398 (mm-30) outliers start: 49 outliers final: 23 residues processed: 312 average time/residue: 1.2992 time to fit residues: 465.7850 Evaluate side-chains 302 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 104 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN H 180 HIS E 38 ASN C 38 ASN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.176596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135973 restraints weight = 23557.621| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.88 r_work: 0.3337 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22816 Z= 0.189 Angle : 0.620 19.584 31023 Z= 0.331 Chirality : 0.044 0.357 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.825 169.494 3832 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 1.86 % Allowed : 17.92 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.33 (0.16), residues: 2594 helix: 1.17 (0.16), residues: 1106 sheet: -0.43 (0.26), residues: 385 loop : -1.61 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 228 HIS 0.009 0.001 HIS H 180 PHE 0.026 0.002 PHE C 29 TYR 0.023 0.002 TYR A 458 ARG 0.008 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1013) hydrogen bonds : angle 5.04348 ( 2929) SS BOND : bond 0.01434 ( 4) SS BOND : angle 7.98477 ( 8) covalent geometry : bond 0.00429 (22811) covalent geometry : angle 0.60627 (31015) Misc. bond : bond 0.00032 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.584 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7072 (pp20) REVERT: A 86 MET cc_start: 0.5078 (mtm) cc_final: 0.4491 (pmm) REVERT: A 171 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: A 243 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7663 (t0) REVERT: A 249 MET cc_start: 0.8573 (tpp) cc_final: 0.8311 (tpp) REVERT: A 430 ASP cc_start: 0.6956 (m-30) cc_final: 0.6624 (m-30) REVERT: A 722 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: B 135 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 200 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 273 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8474 (mm) REVERT: F 1 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6651 (ptp) REVERT: H 116 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: G 159 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7053 (pm20) REVERT: I 122 THR cc_start: 0.5888 (OUTLIER) cc_final: 0.5658 (t) REVERT: E 73 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6964 (m110) REVERT: C 25 ASN cc_start: 0.7775 (t160) cc_final: 0.7429 (t0) REVERT: C 75 ASN cc_start: 0.7570 (p0) cc_final: 0.7168 (t0) REVERT: C 101 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: J 3 LYS cc_start: 0.7768 (mttm) cc_final: 0.7083 (mtpt) REVERT: J 36 VAL cc_start: 0.4549 (t) cc_final: 0.4156 (p) REVERT: J 67 ASP cc_start: 0.4526 (m-30) cc_final: 0.4125 (m-30) REVERT: J 81 MET cc_start: 0.4351 (mpp) cc_final: 0.3908 (mpm) REVERT: J 123 ARG cc_start: 0.6678 (tmm160) cc_final: 0.6116 (mtp85) REVERT: J 162 GLU cc_start: 0.5671 (mm-30) cc_final: 0.5248 (mm-30) outliers start: 42 outliers final: 25 residues processed: 302 average time/residue: 1.2833 time to fit residues: 449.3265 Evaluate side-chains 301 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 109 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 236 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.5446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 HIS C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139207 restraints weight = 23421.396| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.89 r_work: 0.3393 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22816 Z= 0.121 Angle : 0.561 18.915 31023 Z= 0.302 Chirality : 0.042 0.335 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.753 169.220 3832 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 1.77 % Allowed : 18.05 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.19 (0.16), residues: 2594 helix: 1.33 (0.16), residues: 1104 sheet: -0.36 (0.25), residues: 397 loop : -1.59 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 228 HIS 0.009 0.001 HIS H 180 PHE 0.029 0.001 PHE C 29 TYR 0.016 0.001 TYR I 55 ARG 0.006 0.000 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1013) hydrogen bonds : angle 4.86105 ( 2929) SS BOND : bond 0.01150 ( 4) SS BOND : angle 7.56625 ( 8) covalent geometry : bond 0.00256 (22811) covalent geometry : angle 0.54800 (31015) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21400.50 seconds wall clock time: 370 minutes 0.39 seconds (22200.39 seconds total)