Starting phenix.real_space_refine on Thu Jul 31 00:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.map" model { file = "/net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tr1_8454/07_2025/5tr1_8454.cif" } resolution = 3.95 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= 0.003 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8296 2.51 5 N 2058 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12678 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4618 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4618 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.32, per 1000 atoms: 0.66 Number of scatterers: 12678 At special positions: 0 Unit cell: (107.9, 115.7, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2258 8.00 N 2058 7.00 C 8296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 15 sheets defined 57.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 36 through 85 removed outlier: 3.840A pdb=" N CYS A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.554A pdb=" N ARG A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 4.204A pdb=" N ILE A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.557A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 194 through 214 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.603A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.502A pdb=" N TYR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 278 through 313 removed outlier: 3.940A pdb=" N ILE A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 323 through 340 removed outlier: 3.539A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.608A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.618A pdb=" N PHE A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 419 removed outlier: 3.661A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 448 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.917A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 4.028A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.776A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 546 through 551 removed outlier: 4.093A pdb=" N PHE A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.833A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.905A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 85 removed outlier: 3.825A pdb=" N CYS B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 3.556A pdb=" N ARG B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 4.204A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.556A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 185 Processing helix chain 'B' and resid 194 through 214 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.603A pdb=" N GLY B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 221 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.501A pdb=" N TYR B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 278 through 313 removed outlier: 3.941A pdb=" N ILE B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 323 through 340 removed outlier: 3.540A pdb=" N VAL B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.608A pdb=" N LEU B 358 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.616A pdb=" N PHE B 389 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.662A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.918A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.026A pdb=" N LEU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.776A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 Processing helix chain 'B' and resid 546 through 551 removed outlier: 4.093A pdb=" N PHE B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.831A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.904A pdb=" N LEU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.626A pdb=" N VAL A 582 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 579 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 593 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 581 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA3, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.731A pdb=" N GLY A 666 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 73 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.683A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.689A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.112A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.066A pdb=" N TRP L 50 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.626A pdb=" N VAL B 582 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR B 579 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 593 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU B 581 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 660 removed outlier: 3.731A pdb=" N GLY B 666 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.532A pdb=" N GLN I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 73 " --> pdb=" O GLN I 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.683A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.687A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.111A pdb=" N MET M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 53 through 54 removed outlier: 4.066A pdb=" N TRP M 50 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1928 1.31 - 1.44: 3739 1.44 - 1.56: 7217 1.56 - 1.69: 30 1.69 - 1.81: 106 Bond restraints: 13020 Sorted by residual: bond pdb=" CA ILE B 123 " pdb=" CB ILE B 123 " ideal model delta sigma weight residual 1.537 1.564 -0.027 5.00e-03 4.00e+04 2.96e+01 bond pdb=" CA ILE A 123 " pdb=" CB ILE A 123 " ideal model delta sigma weight residual 1.537 1.563 -0.027 5.00e-03 4.00e+04 2.83e+01 bond pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" CA SER B 296 " pdb=" C SER B 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C SER B 64 " pdb=" O SER B 64 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.89e+01 ... (remaining 13015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 13698 1.75 - 3.50: 3543 3.50 - 5.25: 387 5.25 - 7.00: 104 7.00 - 8.75: 24 Bond angle restraints: 17756 Sorted by residual: angle pdb=" O ILE B 123 " pdb=" C ILE B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 120.42 125.59 -5.17 6.40e-01 2.44e+00 6.54e+01 angle pdb=" O ILE A 123 " pdb=" C ILE A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 120.42 125.54 -5.12 6.40e-01 2.44e+00 6.40e+01 angle pdb=" O LEU A 499 " pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 120.27 125.77 -5.50 6.90e-01 2.10e+00 6.35e+01 angle pdb=" O LEU B 499 " pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 120.27 125.72 -5.45 6.90e-01 2.10e+00 6.24e+01 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 111.11 119.86 -8.75 1.20e+00 6.94e-01 5.32e+01 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 6954 16.49 - 32.97: 552 32.97 - 49.46: 120 49.46 - 65.95: 32 65.95 - 82.43: 2 Dihedral angle restraints: 7660 sinusoidal: 2908 harmonic: 4752 Sorted by residual: dihedral pdb=" C THR B 417 " pdb=" N THR B 417 " pdb=" CA THR B 417 " pdb=" CB THR B 417 " ideal model delta harmonic sigma weight residual -122.00 -138.55 16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C THR A 417 " pdb=" N THR A 417 " pdb=" CA THR A 417 " pdb=" CB THR A 417 " ideal model delta harmonic sigma weight residual -122.00 -138.47 16.47 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" C VAL B 174 " pdb=" N VAL B 174 " pdb=" CA VAL B 174 " pdb=" CB VAL B 174 " ideal model delta harmonic sigma weight residual -122.00 -136.99 14.99 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1770 0.123 - 0.247: 224 0.247 - 0.370: 38 0.370 - 0.494: 22 0.494 - 0.617: 2 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA THR B 417 " pdb=" N THR B 417 " pdb=" C THR B 417 " pdb=" CB THR B 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA THR A 417 " pdb=" N THR A 417 " pdb=" C THR A 417 " pdb=" CB THR A 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2053 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 618 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 618 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU A 618 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN A 619 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 618 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU B 618 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU B 618 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 619 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 166 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C VAL B 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY B 167 " -0.018 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 77 2.67 - 3.22: 12159 3.22 - 3.78: 20041 3.78 - 4.34: 25676 4.34 - 4.90: 43062 Nonbonded interactions: 101015 Sorted by model distance: nonbonded pdb=" O ALA B 471 " pdb=" OG SER B 475 " model vdw 2.107 3.040 nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 475 " model vdw 2.107 3.040 nonbonded pdb=" O ALA B 368 " pdb=" OG1 THR B 371 " model vdw 2.363 3.040 nonbonded pdb=" O ALA A 368 " pdb=" OG1 THR A 371 " model vdw 2.364 3.040 nonbonded pdb=" O ILE A 398 " pdb=" OG1 THR A 401 " model vdw 2.401 3.040 ... (remaining 101010 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: 0.07 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'M' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.008 0.069 13024 Z= 0.588 Angle : 1.542 8.754 17764 Z= 1.163 Chirality : 0.095 0.617 2056 Planarity : 0.006 0.057 2188 Dihedral : 12.777 82.433 4592 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 2.23 % Allowed : 7.22 % Favored : 90.55 % Cbeta Deviations : 2.88 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % 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: -0.26 (0.18), residues: 1620 helix: 1.78 (0.14), residues: 814 sheet: -1.22 (0.35), residues: 168 loop : -2.63 (0.20), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 50 HIS 0.006 0.002 HIS B 642 PHE 0.023 0.003 PHE B 410 TYR 0.026 0.002 TYR B 357 ARG 0.005 0.001 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.14474 ( 735) hydrogen bonds : angle 5.43324 ( 2121) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.97728 ( 8) covalent geometry : bond 0.00821 (13020) covalent geometry : angle 1.54234 (17756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8961 (mmm) cc_final: 0.8504 (mmm) REVERT: A 64 SER cc_start: 0.8926 (t) cc_final: 0.8689 (p) REVERT: A 89 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7772 (p90) REVERT: A 96 TRP cc_start: 0.8797 (t-100) cc_final: 0.8489 (t-100) REVERT: A 292 CYS cc_start: 0.8937 (m) cc_final: 0.8629 (m) REVERT: A 297 CYS cc_start: 0.8807 (t) cc_final: 0.8523 (m) REVERT: A 348 MET cc_start: 0.9221 (ttm) cc_final: 0.8899 (ttt) REVERT: A 408 MET cc_start: 0.8766 (mmm) cc_final: 0.8422 (mmm) REVERT: A 411 TRP cc_start: 0.8888 (t60) cc_final: 0.8451 (t60) REVERT: A 412 MET cc_start: 0.9329 (mtp) cc_final: 0.8924 (mtp) REVERT: A 421 MET cc_start: 0.8913 (ptm) cc_final: 0.7584 (ttp) REVERT: H 46 LEU cc_start: 0.8884 (mt) cc_final: 0.8569 (mp) REVERT: H 47 GLU cc_start: 0.8455 (tt0) cc_final: 0.8127 (tm-30) REVERT: H 67 ARG cc_start: 0.8951 (ptp-170) cc_final: 0.8594 (ptp-170) REVERT: H 100 VAL cc_start: 0.8931 (p) cc_final: 0.8690 (p) REVERT: H 101 ASP cc_start: 0.8968 (m-30) cc_final: 0.8706 (m-30) REVERT: L 11 MET cc_start: 0.8935 (mmm) cc_final: 0.8394 (mpp) REVERT: L 55 TYR cc_start: 0.8674 (t80) cc_final: 0.7576 (t80) REVERT: L 77 ASN cc_start: 0.9067 (m-40) cc_final: 0.8831 (p0) REVERT: L 89 GLN cc_start: 0.9046 (tt0) cc_final: 0.8536 (tm-30) REVERT: L 90 GLN cc_start: 0.9197 (pt0) cc_final: 0.8501 (pp30) REVERT: L 96 LEU cc_start: 0.9498 (mt) cc_final: 0.9295 (mt) REVERT: L 104 LEU cc_start: 0.8540 (tp) cc_final: 0.7991 (tp) REVERT: L 105 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7642 (tp30) REVERT: B 60 MET cc_start: 0.8973 (mmm) cc_final: 0.8546 (mmm) REVERT: B 64 SER cc_start: 0.8922 (t) cc_final: 0.8686 (p) REVERT: B 96 TRP cc_start: 0.8703 (t-100) cc_final: 0.8420 (t-100) REVERT: B 292 CYS cc_start: 0.8914 (m) cc_final: 0.8605 (m) REVERT: B 297 CYS cc_start: 0.8787 (t) cc_final: 0.8506 (m) REVERT: B 348 MET cc_start: 0.9224 (ttm) cc_final: 0.8907 (ttt) REVERT: B 408 MET cc_start: 0.8775 (mmm) cc_final: 0.8447 (mmm) REVERT: B 411 TRP cc_start: 0.8885 (t60) cc_final: 0.8463 (t60) REVERT: B 412 MET cc_start: 0.9326 (mtp) cc_final: 0.8927 (mtp) REVERT: B 421 MET cc_start: 0.8900 (ptm) cc_final: 0.7599 (ttp) REVERT: I 46 LEU cc_start: 0.8908 (mt) cc_final: 0.8613 (mp) REVERT: I 47 GLU cc_start: 0.8449 (tt0) cc_final: 0.8111 (tm-30) REVERT: I 49 MET cc_start: 0.9321 (mmm) cc_final: 0.9069 (mmm) REVERT: I 67 ARG cc_start: 0.8960 (ptp-170) cc_final: 0.8554 (ptp-170) REVERT: I 100 VAL cc_start: 0.8957 (p) cc_final: 0.8713 (p) REVERT: I 101 ASP cc_start: 0.8969 (m-30) cc_final: 0.8731 (m-30) REVERT: M 11 MET cc_start: 0.8936 (mmm) cc_final: 0.8400 (mpp) REVERT: M 55 TYR cc_start: 0.8689 (t80) cc_final: 0.7571 (t80) REVERT: M 77 ASN cc_start: 0.9064 (m-40) cc_final: 0.8832 (p0) REVERT: M 89 GLN cc_start: 0.9017 (tt0) cc_final: 0.8491 (tm-30) REVERT: M 90 GLN cc_start: 0.9213 (pt0) cc_final: 0.8523 (pp30) REVERT: M 96 LEU cc_start: 0.9505 (mt) cc_final: 0.9264 (mt) REVERT: M 104 LEU cc_start: 0.8546 (tp) cc_final: 0.7928 (tp) REVERT: M 105 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7538 (tp30) outliers start: 30 outliers final: 8 residues processed: 302 average time/residue: 0.2627 time to fit residues: 112.5067 Evaluate side-chains 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 313 ASN A 564 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN B 303 GLN B 313 ASN B 564 GLN I 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.035133 restraints weight = 88374.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.036201 restraints weight = 45239.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.037032 restraints weight = 28056.329| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13024 Z= 0.144 Angle : 0.648 7.456 17764 Z= 0.329 Chirality : 0.042 0.266 2056 Planarity : 0.005 0.048 2188 Dihedral : 6.296 55.170 1898 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.23 % Allowed : 14.29 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1620 helix: 3.56 (0.18), residues: 826 sheet: -0.95 (0.33), residues: 182 loop : -1.98 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 234 HIS 0.004 0.001 HIS B 642 PHE 0.014 0.001 PHE I 79 TYR 0.020 0.001 TYR B 99 ARG 0.005 0.001 ARG B 595 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 735) hydrogen bonds : angle 4.47434 ( 2121) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.61466 ( 8) covalent geometry : bond 0.00319 (13020) covalent geometry : angle 0.64847 (17756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8931 (mmm) cc_final: 0.8541 (mmm) REVERT: A 64 SER cc_start: 0.9256 (t) cc_final: 0.8953 (p) REVERT: A 212 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 354 MET cc_start: 0.8971 (mmt) cc_final: 0.8756 (tpt) REVERT: A 363 ASP cc_start: 0.8244 (t0) cc_final: 0.8030 (t0) REVERT: A 412 MET cc_start: 0.9267 (mtp) cc_final: 0.8481 (mtp) REVERT: A 421 MET cc_start: 0.7951 (ptm) cc_final: 0.7340 (ttp) REVERT: H 47 GLU cc_start: 0.7921 (tt0) cc_final: 0.7701 (tt0) REVERT: H 49 MET cc_start: 0.8877 (mmm) cc_final: 0.8555 (mtt) REVERT: H 101 ASP cc_start: 0.7767 (m-30) cc_final: 0.6735 (m-30) REVERT: L 27 GLN cc_start: 0.8727 (mt0) cc_final: 0.8472 (mt0) REVERT: L 55 TYR cc_start: 0.7883 (t80) cc_final: 0.7098 (t80) REVERT: L 89 GLN cc_start: 0.8746 (tt0) cc_final: 0.8277 (tm-30) REVERT: L 96 LEU cc_start: 0.9384 (mt) cc_final: 0.9162 (mt) REVERT: L 106 LEU cc_start: 0.8406 (tt) cc_final: 0.7936 (tt) REVERT: B 60 MET cc_start: 0.8951 (mmm) cc_final: 0.8571 (mmm) REVERT: B 64 SER cc_start: 0.9351 (t) cc_final: 0.9013 (p) REVERT: B 212 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 320 MET cc_start: 0.8934 (tpp) cc_final: 0.8732 (tpp) REVERT: B 354 MET cc_start: 0.8978 (mmt) cc_final: 0.8759 (tpt) REVERT: B 408 MET cc_start: 0.8966 (mmm) cc_final: 0.8765 (mmm) REVERT: B 412 MET cc_start: 0.9253 (mtp) cc_final: 0.8484 (mtp) REVERT: B 421 MET cc_start: 0.7958 (ptm) cc_final: 0.7337 (ttp) REVERT: I 101 ASP cc_start: 0.7820 (m-30) cc_final: 0.6794 (m-30) REVERT: M 27 GLN cc_start: 0.8731 (mt0) cc_final: 0.8484 (mt0) REVERT: M 55 TYR cc_start: 0.7875 (t80) cc_final: 0.7063 (t80) REVERT: M 89 GLN cc_start: 0.8734 (tt0) cc_final: 0.8324 (tm-30) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.2518 time to fit residues: 65.6457 Evaluate side-chains 130 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 497 HIS H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 497 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.033790 restraints weight = 89264.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.034834 restraints weight = 46090.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035517 restraints weight = 28802.914| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13024 Z= 0.162 Angle : 0.611 6.742 17764 Z= 0.309 Chirality : 0.040 0.194 2056 Planarity : 0.004 0.039 2188 Dihedral : 5.273 47.579 1886 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.39 % Allowed : 14.21 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1620 helix: 3.31 (0.18), residues: 826 sheet: -1.11 (0.34), residues: 196 loop : -1.72 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 411 HIS 0.002 0.001 HIS A 549 PHE 0.011 0.001 PHE L 98 TYR 0.023 0.002 TYR H 33 ARG 0.005 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 735) hydrogen bonds : angle 4.30091 ( 2121) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.71116 ( 8) covalent geometry : bond 0.00367 (13020) covalent geometry : angle 0.61048 (17756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9031 (mmm) cc_final: 0.8665 (mmm) REVERT: A 64 SER cc_start: 0.9339 (t) cc_final: 0.9044 (p) REVERT: A 180 LEU cc_start: 0.9522 (mm) cc_final: 0.8986 (tt) REVERT: A 212 VAL cc_start: 0.8625 (p) cc_final: 0.8338 (m) REVERT: A 354 MET cc_start: 0.8893 (mmt) cc_final: 0.8484 (tpp) REVERT: A 359 ASP cc_start: 0.8956 (m-30) cc_final: 0.8686 (m-30) REVERT: A 421 MET cc_start: 0.8012 (ptm) cc_final: 0.6951 (ttm) REVERT: A 538 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7353 (ptm-80) REVERT: H 47 GLU cc_start: 0.8263 (tt0) cc_final: 0.7861 (tt0) REVERT: H 49 MET cc_start: 0.8893 (mmm) cc_final: 0.8494 (mtt) REVERT: H 101 ASP cc_start: 0.8056 (m-30) cc_final: 0.7371 (m-30) REVERT: L 52 SER cc_start: 0.8938 (t) cc_final: 0.8738 (p) REVERT: L 55 TYR cc_start: 0.7750 (t80) cc_final: 0.7054 (t80) REVERT: L 89 GLN cc_start: 0.8725 (tt0) cc_final: 0.8478 (tt0) REVERT: L 106 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8125 (tt) REVERT: L 107 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.5810 (mmmt) REVERT: B 60 MET cc_start: 0.9021 (mmm) cc_final: 0.8656 (mmm) REVERT: B 64 SER cc_start: 0.9390 (t) cc_final: 0.9079 (p) REVERT: B 175 MET cc_start: 0.8956 (ttm) cc_final: 0.8286 (mtp) REVERT: B 180 LEU cc_start: 0.9498 (mm) cc_final: 0.8942 (tt) REVERT: B 212 VAL cc_start: 0.8614 (p) cc_final: 0.8325 (m) REVERT: B 320 MET cc_start: 0.9087 (tpp) cc_final: 0.8884 (tpp) REVERT: B 354 MET cc_start: 0.8912 (mmt) cc_final: 0.8493 (tpp) REVERT: B 359 ASP cc_start: 0.8965 (m-30) cc_final: 0.8673 (m-30) REVERT: B 421 MET cc_start: 0.8003 (ptm) cc_final: 0.6990 (ttm) REVERT: B 538 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7449 (ptm-80) REVERT: I 49 MET cc_start: 0.8538 (mmm) cc_final: 0.8337 (mmm) REVERT: I 101 ASP cc_start: 0.8056 (m-30) cc_final: 0.7351 (m-30) REVERT: M 55 TYR cc_start: 0.7820 (t80) cc_final: 0.7090 (t80) REVERT: M 89 GLN cc_start: 0.8771 (tt0) cc_final: 0.8525 (tt0) outliers start: 59 outliers final: 27 residues processed: 170 average time/residue: 0.2327 time to fit residues: 59.4918 Evaluate side-chains 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.033466 restraints weight = 89573.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.034542 restraints weight = 45609.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.035288 restraints weight = 28306.347| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13024 Z= 0.163 Angle : 0.596 7.111 17764 Z= 0.302 Chirality : 0.040 0.199 2056 Planarity : 0.004 0.034 2188 Dihedral : 5.382 57.314 1886 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 14.66 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1620 helix: 2.95 (0.18), residues: 830 sheet: -1.02 (0.33), residues: 216 loop : -1.61 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 48 HIS 0.004 0.001 HIS B 497 PHE 0.009 0.001 PHE I 79 TYR 0.014 0.002 TYR H 33 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 735) hydrogen bonds : angle 4.27894 ( 2121) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.60102 ( 8) covalent geometry : bond 0.00363 (13020) covalent geometry : angle 0.59613 (17756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9374 (t) cc_final: 0.9086 (p) REVERT: A 175 MET cc_start: 0.8950 (ttm) cc_final: 0.8239 (mtp) REVERT: A 212 VAL cc_start: 0.8482 (p) cc_final: 0.8183 (m) REVERT: A 354 MET cc_start: 0.8922 (mmt) cc_final: 0.8545 (tpp) REVERT: A 359 ASP cc_start: 0.8950 (m-30) cc_final: 0.8605 (m-30) REVERT: A 421 MET cc_start: 0.7982 (ptm) cc_final: 0.7293 (ttp) REVERT: H 33 TYR cc_start: 0.8304 (m-80) cc_final: 0.7899 (m-80) REVERT: H 47 GLU cc_start: 0.8136 (tt0) cc_final: 0.7852 (tt0) REVERT: H 49 MET cc_start: 0.9030 (mmm) cc_final: 0.8645 (mtt) REVERT: H 101 ASP cc_start: 0.8276 (m-30) cc_final: 0.7421 (m-30) REVERT: L 55 TYR cc_start: 0.7793 (t80) cc_final: 0.7066 (t80) REVERT: L 89 GLN cc_start: 0.8836 (tt0) cc_final: 0.8373 (tm-30) REVERT: L 106 LEU cc_start: 0.8408 (tt) cc_final: 0.8198 (tt) REVERT: B 64 SER cc_start: 0.9348 (t) cc_final: 0.9055 (p) REVERT: B 212 VAL cc_start: 0.8455 (p) cc_final: 0.8178 (m) REVERT: B 354 MET cc_start: 0.8913 (mmt) cc_final: 0.8535 (tpp) REVERT: B 359 ASP cc_start: 0.8945 (m-30) cc_final: 0.8584 (m-30) REVERT: B 421 MET cc_start: 0.7982 (ptm) cc_final: 0.7296 (ttp) REVERT: I 33 TYR cc_start: 0.8324 (m-80) cc_final: 0.7966 (m-80) REVERT: I 45 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8444 (mmtt) REVERT: I 49 MET cc_start: 0.8619 (mmm) cc_final: 0.8350 (mmm) REVERT: I 101 ASP cc_start: 0.8253 (m-30) cc_final: 0.7398 (m-30) REVERT: M 55 TYR cc_start: 0.7849 (t80) cc_final: 0.7066 (t80) REVERT: M 89 GLN cc_start: 0.8847 (tt0) cc_final: 0.8286 (tm-30) outliers start: 41 outliers final: 29 residues processed: 153 average time/residue: 0.2246 time to fit residues: 51.7470 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 0.0000 chunk 32 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.039367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.033462 restraints weight = 90769.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.034492 restraints weight = 47355.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.035186 restraints weight = 29626.677| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13024 Z= 0.156 Angle : 0.600 12.806 17764 Z= 0.297 Chirality : 0.039 0.186 2056 Planarity : 0.004 0.033 2188 Dihedral : 5.232 56.499 1886 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.72 % Allowed : 14.43 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1620 helix: 3.02 (0.18), residues: 814 sheet: -0.99 (0.34), residues: 216 loop : -1.45 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 48 HIS 0.003 0.001 HIS B 497 PHE 0.010 0.001 PHE A 432 TYR 0.013 0.002 TYR H 33 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 735) hydrogen bonds : angle 4.23894 ( 2121) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.55258 ( 8) covalent geometry : bond 0.00351 (13020) covalent geometry : angle 0.59978 (17756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 115 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9380 (t) cc_final: 0.9100 (p) REVERT: A 175 MET cc_start: 0.8924 (ttm) cc_final: 0.8177 (mtp) REVERT: A 212 VAL cc_start: 0.8477 (p) cc_final: 0.8211 (m) REVERT: A 354 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: A 359 ASP cc_start: 0.8948 (m-30) cc_final: 0.8562 (m-30) REVERT: A 411 TRP cc_start: 0.8334 (t60) cc_final: 0.8068 (t60) REVERT: A 421 MET cc_start: 0.7920 (ptm) cc_final: 0.7299 (ttp) REVERT: A 440 LEU cc_start: 0.9176 (mm) cc_final: 0.8974 (tt) REVERT: H 33 TYR cc_start: 0.8407 (m-80) cc_final: 0.7983 (m-80) REVERT: H 45 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8631 (mtmm) REVERT: H 47 GLU cc_start: 0.8278 (tt0) cc_final: 0.7983 (tt0) REVERT: H 49 MET cc_start: 0.8847 (mmm) cc_final: 0.8590 (mtt) REVERT: H 101 ASP cc_start: 0.7984 (m-30) cc_final: 0.7083 (m-30) REVERT: L 55 TYR cc_start: 0.7734 (t80) cc_final: 0.6971 (t80) REVERT: L 89 GLN cc_start: 0.8777 (tt0) cc_final: 0.8210 (tm-30) REVERT: L 106 LEU cc_start: 0.8400 (tt) cc_final: 0.8176 (tt) REVERT: L 107 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5309 (tptp) REVERT: B 60 MET cc_start: 0.9168 (mmm) cc_final: 0.8906 (mmm) REVERT: B 64 SER cc_start: 0.9383 (t) cc_final: 0.9104 (p) REVERT: B 175 MET cc_start: 0.8902 (ttm) cc_final: 0.8235 (mtp) REVERT: B 212 VAL cc_start: 0.8491 (p) cc_final: 0.8225 (m) REVERT: B 354 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8531 (tpp) REVERT: B 359 ASP cc_start: 0.8939 (m-30) cc_final: 0.8545 (m-30) REVERT: B 421 MET cc_start: 0.7966 (ptm) cc_final: 0.7313 (ttp) REVERT: B 440 LEU cc_start: 0.9174 (mm) cc_final: 0.8967 (tt) REVERT: I 3 GLN cc_start: 0.8464 (tp40) cc_final: 0.8096 (tm-30) REVERT: I 45 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8581 (mtmm) REVERT: I 101 ASP cc_start: 0.7950 (m-30) cc_final: 0.6964 (m-30) REVERT: M 55 TYR cc_start: 0.7744 (t80) cc_final: 0.6907 (t80) outliers start: 50 outliers final: 35 residues processed: 150 average time/residue: 0.2248 time to fit residues: 51.4490 Evaluate side-chains 138 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 62 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.033461 restraints weight = 93213.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.034541 restraints weight = 47404.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.035367 restraints weight = 29453.490| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13024 Z= 0.145 Angle : 0.570 11.654 17764 Z= 0.285 Chirality : 0.038 0.191 2056 Planarity : 0.004 0.034 2188 Dihedral : 5.213 57.281 1886 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.42 % Allowed : 14.73 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1620 helix: 2.98 (0.18), residues: 814 sheet: -0.91 (0.34), residues: 216 loop : -1.43 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 48 HIS 0.003 0.001 HIS B 497 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR B 99 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 735) hydrogen bonds : angle 4.16109 ( 2121) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.61837 ( 8) covalent geometry : bond 0.00327 (13020) covalent geometry : angle 0.56952 (17756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9391 (t) cc_final: 0.9102 (p) REVERT: A 175 MET cc_start: 0.8926 (ttm) cc_final: 0.8194 (mtp) REVERT: A 212 VAL cc_start: 0.8484 (p) cc_final: 0.8205 (m) REVERT: A 348 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8643 (tpp) REVERT: A 354 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8558 (tpp) REVERT: A 359 ASP cc_start: 0.8954 (m-30) cc_final: 0.8522 (m-30) REVERT: A 396 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7686 (m-10) REVERT: A 421 MET cc_start: 0.7924 (ptm) cc_final: 0.7292 (ttp) REVERT: A 503 MET cc_start: 0.8987 (mtp) cc_final: 0.8702 (mtm) REVERT: H 45 LYS cc_start: 0.8986 (ptpp) cc_final: 0.8687 (mtmm) REVERT: H 47 GLU cc_start: 0.8283 (tt0) cc_final: 0.7916 (tt0) REVERT: H 49 MET cc_start: 0.8850 (mmm) cc_final: 0.8549 (mtt) REVERT: H 101 ASP cc_start: 0.8269 (m-30) cc_final: 0.7275 (m-30) REVERT: L 55 TYR cc_start: 0.7754 (t80) cc_final: 0.6939 (t80) REVERT: L 89 GLN cc_start: 0.8730 (tt0) cc_final: 0.8075 (tm-30) REVERT: L 106 LEU cc_start: 0.8506 (tt) cc_final: 0.8238 (tt) REVERT: L 107 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.5845 (tptp) REVERT: B 64 SER cc_start: 0.9357 (t) cc_final: 0.9059 (p) REVERT: B 175 MET cc_start: 0.8931 (ttm) cc_final: 0.8213 (mtp) REVERT: B 212 VAL cc_start: 0.8453 (p) cc_final: 0.8192 (m) REVERT: B 348 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8556 (tpp) REVERT: B 354 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8560 (tpp) REVERT: B 359 ASP cc_start: 0.8953 (m-30) cc_final: 0.8523 (m-30) REVERT: B 396 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: B 412 MET cc_start: 0.9375 (mtt) cc_final: 0.9066 (mtt) REVERT: B 421 MET cc_start: 0.7938 (ptm) cc_final: 0.7308 (ttp) REVERT: I 3 GLN cc_start: 0.8462 (tp40) cc_final: 0.8070 (tm-30) REVERT: I 101 ASP cc_start: 0.7972 (m-30) cc_final: 0.6985 (m-30) REVERT: M 55 TYR cc_start: 0.7792 (t80) cc_final: 0.6911 (t80) REVERT: M 89 GLN cc_start: 0.8654 (tt0) cc_final: 0.8255 (tt0) outliers start: 46 outliers final: 30 residues processed: 143 average time/residue: 0.2383 time to fit residues: 50.6976 Evaluate side-chains 133 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 61 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.034586 restraints weight = 88476.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.035670 restraints weight = 45395.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036375 restraints weight = 28382.194| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13024 Z= 0.106 Angle : 0.559 11.514 17764 Z= 0.275 Chirality : 0.038 0.195 2056 Planarity : 0.004 0.033 2188 Dihedral : 5.013 55.886 1886 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.53 % Allowed : 15.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1620 helix: 2.91 (0.18), residues: 822 sheet: -0.72 (0.34), residues: 218 loop : -1.38 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 48 HIS 0.003 0.000 HIS B 171 PHE 0.008 0.001 PHE M 98 TYR 0.016 0.001 TYR A 99 ARG 0.004 0.000 ARG I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 735) hydrogen bonds : angle 4.04412 ( 2121) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.70231 ( 8) covalent geometry : bond 0.00238 (13020) covalent geometry : angle 0.55844 (17756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.480 Fit side-chains REVERT: A 64 SER cc_start: 0.9357 (t) cc_final: 0.9045 (p) REVERT: A 175 MET cc_start: 0.8898 (ttm) cc_final: 0.8173 (mtp) REVERT: A 180 LEU cc_start: 0.9488 (mm) cc_final: 0.8994 (tt) REVERT: A 212 VAL cc_start: 0.8432 (p) cc_final: 0.8173 (m) REVERT: A 348 MET cc_start: 0.9160 (ttt) cc_final: 0.8537 (tpp) REVERT: A 354 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8611 (tpp) REVERT: A 359 ASP cc_start: 0.8767 (m-30) cc_final: 0.8304 (m-30) REVERT: A 396 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: A 411 TRP cc_start: 0.8367 (t60) cc_final: 0.7594 (t60) REVERT: A 412 MET cc_start: 0.9415 (mtt) cc_final: 0.8288 (mmt) REVERT: A 421 MET cc_start: 0.8015 (ptm) cc_final: 0.7417 (ttp) REVERT: A 503 MET cc_start: 0.8948 (mtp) cc_final: 0.8605 (mtm) REVERT: H 33 TYR cc_start: 0.8370 (m-80) cc_final: 0.7961 (m-80) REVERT: H 45 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8524 (mtmm) REVERT: H 47 GLU cc_start: 0.8206 (tt0) cc_final: 0.7863 (tt0) REVERT: H 49 MET cc_start: 0.8731 (mmm) cc_final: 0.8508 (mtt) REVERT: H 101 ASP cc_start: 0.8047 (m-30) cc_final: 0.6952 (m-30) REVERT: L 55 TYR cc_start: 0.7759 (t80) cc_final: 0.6877 (t80) REVERT: L 89 GLN cc_start: 0.8665 (tt0) cc_final: 0.8041 (tm-30) REVERT: B 64 SER cc_start: 0.9351 (t) cc_final: 0.9047 (p) REVERT: B 175 MET cc_start: 0.8897 (ttm) cc_final: 0.8275 (mtp) REVERT: B 180 LEU cc_start: 0.9487 (mm) cc_final: 0.8997 (tt) REVERT: B 212 VAL cc_start: 0.8436 (p) cc_final: 0.8162 (m) REVERT: B 348 MET cc_start: 0.9172 (ttt) cc_final: 0.8661 (tpp) REVERT: B 354 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: B 359 ASP cc_start: 0.8759 (m-30) cc_final: 0.8292 (m-30) REVERT: B 396 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: B 412 MET cc_start: 0.9371 (mtt) cc_final: 0.9015 (mtt) REVERT: B 421 MET cc_start: 0.8058 (ptm) cc_final: 0.7401 (ttp) REVERT: B 503 MET cc_start: 0.8971 (mtp) cc_final: 0.8638 (mtm) REVERT: I 3 GLN cc_start: 0.8518 (tp40) cc_final: 0.8136 (tm-30) REVERT: I 33 TYR cc_start: 0.8404 (m-80) cc_final: 0.8105 (m-80) REVERT: I 45 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8320 (mtmm) REVERT: I 101 ASP cc_start: 0.8039 (m-30) cc_final: 0.6968 (m-30) REVERT: M 55 TYR cc_start: 0.7778 (t80) cc_final: 0.6875 (t80) REVERT: M 89 GLN cc_start: 0.8623 (tt0) cc_final: 0.8039 (tm-30) REVERT: M 104 LEU cc_start: 0.8306 (tp) cc_final: 0.7997 (tt) outliers start: 34 outliers final: 22 residues processed: 153 average time/residue: 0.2322 time to fit residues: 53.6090 Evaluate side-chains 139 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN B 543 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.039799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.033845 restraints weight = 92280.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034891 restraints weight = 47069.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.035639 restraints weight = 29214.911| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13024 Z= 0.140 Angle : 0.585 11.757 17764 Z= 0.285 Chirality : 0.038 0.184 2056 Planarity : 0.004 0.035 2188 Dihedral : 5.016 56.003 1886 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.75 % Allowed : 15.33 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1620 helix: 2.98 (0.18), residues: 814 sheet: -0.60 (0.35), residues: 218 loop : -1.26 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 48 HIS 0.003 0.001 HIS A 364 PHE 0.011 0.001 PHE I 79 TYR 0.012 0.001 TYR A 99 ARG 0.003 0.000 ARG I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 735) hydrogen bonds : angle 4.08318 ( 2121) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.52432 ( 8) covalent geometry : bond 0.00318 (13020) covalent geometry : angle 0.58504 (17756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.396 Fit side-chains REVERT: A 64 SER cc_start: 0.9370 (t) cc_final: 0.9067 (p) REVERT: A 175 MET cc_start: 0.8931 (ttm) cc_final: 0.8119 (mtp) REVERT: A 348 MET cc_start: 0.9151 (ttt) cc_final: 0.8568 (tpp) REVERT: A 354 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8582 (tpp) REVERT: A 359 ASP cc_start: 0.8903 (m-30) cc_final: 0.8453 (m-30) REVERT: A 396 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7973 (m-10) REVERT: A 411 TRP cc_start: 0.8429 (t60) cc_final: 0.7676 (t60) REVERT: A 412 MET cc_start: 0.9408 (mtt) cc_final: 0.8190 (mmt) REVERT: A 421 MET cc_start: 0.8100 (ptm) cc_final: 0.7450 (ttp) REVERT: A 479 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9019 (p) REVERT: A 503 MET cc_start: 0.9056 (mtp) cc_final: 0.8693 (mtm) REVERT: A 576 MET cc_start: 0.7554 (ppp) cc_final: 0.7280 (ppp) REVERT: H 45 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8654 (mtmm) REVERT: H 47 GLU cc_start: 0.8202 (tt0) cc_final: 0.7846 (tt0) REVERT: H 101 ASP cc_start: 0.8359 (m-30) cc_final: 0.7582 (m-30) REVERT: L 55 TYR cc_start: 0.7797 (t80) cc_final: 0.7328 (t80) REVERT: L 89 GLN cc_start: 0.8673 (tt0) cc_final: 0.8388 (tt0) REVERT: B 60 MET cc_start: 0.9201 (mmm) cc_final: 0.8966 (mmm) REVERT: B 64 SER cc_start: 0.9364 (t) cc_final: 0.9063 (p) REVERT: B 175 MET cc_start: 0.8884 (ttm) cc_final: 0.8265 (mtp) REVERT: B 348 MET cc_start: 0.9187 (ttt) cc_final: 0.8735 (tpp) REVERT: B 354 MET cc_start: 0.8962 (mmt) cc_final: 0.8571 (tpp) REVERT: B 359 ASP cc_start: 0.8759 (m-30) cc_final: 0.8297 (m-30) REVERT: B 396 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 412 MET cc_start: 0.9375 (mtt) cc_final: 0.9037 (mtt) REVERT: B 421 MET cc_start: 0.8044 (ptm) cc_final: 0.7431 (ttp) REVERT: B 503 MET cc_start: 0.9059 (mtp) cc_final: 0.8709 (mtm) REVERT: B 576 MET cc_start: 0.7355 (ppp) cc_final: 0.7068 (ppp) REVERT: I 3 GLN cc_start: 0.8565 (tp40) cc_final: 0.8157 (tm-30) REVERT: I 45 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8387 (mtmm) REVERT: I 101 ASP cc_start: 0.8167 (m-30) cc_final: 0.7401 (m-30) REVERT: M 55 TYR cc_start: 0.7789 (t80) cc_final: 0.7380 (t80) REVERT: M 89 GLN cc_start: 0.8697 (tt0) cc_final: 0.8033 (tm-30) outliers start: 37 outliers final: 25 residues processed: 132 average time/residue: 0.2246 time to fit residues: 45.4329 Evaluate side-chains 132 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.034547 restraints weight = 90537.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035610 restraints weight = 46217.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.036424 restraints weight = 28707.936| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13024 Z= 0.112 Angle : 0.601 12.802 17764 Z= 0.284 Chirality : 0.038 0.188 2056 Planarity : 0.004 0.035 2188 Dihedral : 4.879 54.021 1886 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 15.77 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1620 helix: 2.92 (0.18), residues: 816 sheet: -0.45 (0.35), residues: 218 loop : -1.20 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 48 HIS 0.002 0.001 HIS B 497 PHE 0.009 0.001 PHE H 79 TYR 0.015 0.001 TYR A 99 ARG 0.004 0.000 ARG I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 735) hydrogen bonds : angle 4.01426 ( 2121) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.56339 ( 8) covalent geometry : bond 0.00256 (13020) covalent geometry : angle 0.60137 (17756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9369 (t) cc_final: 0.9058 (p) REVERT: A 175 MET cc_start: 0.8913 (ttm) cc_final: 0.8100 (mtp) REVERT: A 212 VAL cc_start: 0.8370 (p) cc_final: 0.8114 (m) REVERT: A 348 MET cc_start: 0.9138 (ttt) cc_final: 0.8633 (tpp) REVERT: A 354 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8611 (tpp) REVERT: A 359 ASP cc_start: 0.8911 (m-30) cc_final: 0.8444 (m-30) REVERT: A 396 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: A 411 TRP cc_start: 0.8296 (t60) cc_final: 0.7997 (t60) REVERT: A 421 MET cc_start: 0.8148 (ptm) cc_final: 0.7591 (ttp) REVERT: A 479 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9037 (p) REVERT: A 503 MET cc_start: 0.9051 (mtp) cc_final: 0.8673 (mtm) REVERT: A 576 MET cc_start: 0.7543 (ppp) cc_final: 0.7310 (ppp) REVERT: H 45 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8596 (mtmm) REVERT: H 101 ASP cc_start: 0.8311 (m-30) cc_final: 0.7549 (m-30) REVERT: L 55 TYR cc_start: 0.7767 (t80) cc_final: 0.7277 (t80) REVERT: L 89 GLN cc_start: 0.8642 (tt0) cc_final: 0.8104 (tm-30) REVERT: L 104 LEU cc_start: 0.8425 (tp) cc_final: 0.8195 (tt) REVERT: B 64 SER cc_start: 0.9359 (t) cc_final: 0.9052 (p) REVERT: B 175 MET cc_start: 0.8910 (ttm) cc_final: 0.8256 (mtp) REVERT: B 212 VAL cc_start: 0.8353 (p) cc_final: 0.8105 (m) REVERT: B 348 MET cc_start: 0.9171 (ttt) cc_final: 0.8718 (tpp) REVERT: B 354 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: B 359 ASP cc_start: 0.8910 (m-30) cc_final: 0.8439 (m-30) REVERT: B 396 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: B 412 MET cc_start: 0.9361 (mtt) cc_final: 0.9043 (mtt) REVERT: B 421 MET cc_start: 0.8054 (ptm) cc_final: 0.7458 (ttp) REVERT: B 479 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9035 (p) REVERT: B 503 MET cc_start: 0.9064 (mtp) cc_final: 0.8686 (mtm) REVERT: B 576 MET cc_start: 0.7551 (ppp) cc_final: 0.7312 (ppp) REVERT: I 3 GLN cc_start: 0.8598 (tp40) cc_final: 0.8212 (tm-30) REVERT: I 45 LYS cc_start: 0.8764 (ptpp) cc_final: 0.8336 (mtmm) REVERT: I 101 ASP cc_start: 0.8124 (m-30) cc_final: 0.7385 (m-30) REVERT: M 55 TYR cc_start: 0.7789 (t80) cc_final: 0.7344 (t80) REVERT: M 89 GLN cc_start: 0.8671 (tt0) cc_final: 0.8059 (tm-30) outliers start: 35 outliers final: 22 residues processed: 134 average time/residue: 0.2127 time to fit residues: 44.6142 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 0.0020 chunk 55 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.033287 restraints weight = 91546.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.034320 restraints weight = 47055.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.035082 restraints weight = 29378.347| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13024 Z= 0.190 Angle : 0.641 11.866 17764 Z= 0.310 Chirality : 0.039 0.188 2056 Planarity : 0.004 0.036 2188 Dihedral : 5.084 55.157 1886 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.60 % Allowed : 15.77 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1620 helix: 2.90 (0.18), residues: 810 sheet: -0.50 (0.36), residues: 218 loop : -1.13 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 48 HIS 0.003 0.001 HIS A 497 PHE 0.010 0.001 PHE A 432 TYR 0.013 0.002 TYR H 33 ARG 0.004 0.001 ARG H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 735) hydrogen bonds : angle 4.15850 ( 2121) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.54867 ( 8) covalent geometry : bond 0.00423 (13020) covalent geometry : angle 0.64121 (17756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9369 (t) cc_final: 0.9062 (p) REVERT: A 175 MET cc_start: 0.8916 (ttm) cc_final: 0.8096 (mtp) REVERT: A 348 MET cc_start: 0.9140 (ttt) cc_final: 0.8621 (tpp) REVERT: A 354 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: A 359 ASP cc_start: 0.8952 (m-30) cc_final: 0.8495 (m-30) REVERT: A 396 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: A 411 TRP cc_start: 0.8375 (t60) cc_final: 0.8164 (t60) REVERT: A 421 MET cc_start: 0.8002 (ptm) cc_final: 0.7449 (ttp) REVERT: A 440 LEU cc_start: 0.9220 (mm) cc_final: 0.8991 (tt) REVERT: A 503 MET cc_start: 0.9017 (mtp) cc_final: 0.8717 (mtm) REVERT: H 101 ASP cc_start: 0.8280 (m-30) cc_final: 0.7651 (m-30) REVERT: L 55 TYR cc_start: 0.7873 (t80) cc_final: 0.7392 (t80) REVERT: L 89 GLN cc_start: 0.8764 (tt0) cc_final: 0.8466 (tt0) REVERT: B 64 SER cc_start: 0.9382 (t) cc_final: 0.9082 (p) REVERT: B 175 MET cc_start: 0.8859 (ttm) cc_final: 0.8227 (mtp) REVERT: B 354 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8598 (tpp) REVERT: B 359 ASP cc_start: 0.8943 (m-30) cc_final: 0.8483 (m-30) REVERT: B 396 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: B 412 MET cc_start: 0.9376 (mtt) cc_final: 0.9017 (mtt) REVERT: B 421 MET cc_start: 0.7949 (ptm) cc_final: 0.6823 (ttm) REVERT: B 440 LEU cc_start: 0.9233 (mm) cc_final: 0.8983 (tt) REVERT: B 503 MET cc_start: 0.9039 (mtp) cc_final: 0.8750 (mtm) REVERT: I 3 GLN cc_start: 0.8613 (tp40) cc_final: 0.8191 (tm-30) REVERT: I 101 ASP cc_start: 0.8124 (m-30) cc_final: 0.7518 (m-30) REVERT: M 55 TYR cc_start: 0.7859 (t80) cc_final: 0.7384 (t80) REVERT: M 89 GLN cc_start: 0.8738 (tt0) cc_final: 0.8325 (tt0) outliers start: 35 outliers final: 22 residues processed: 121 average time/residue: 0.2191 time to fit residues: 40.6895 Evaluate side-chains 120 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 4 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.040174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.034303 restraints weight = 90305.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.035349 restraints weight = 47122.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.036143 restraints weight = 29579.217| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13024 Z= 0.120 Angle : 0.625 12.785 17764 Z= 0.292 Chirality : 0.038 0.185 2056 Planarity : 0.004 0.036 2188 Dihedral : 4.884 52.154 1886 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.16 % Allowed : 16.37 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1620 helix: 2.81 (0.18), residues: 818 sheet: -0.34 (0.37), residues: 218 loop : -1.12 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 48 HIS 0.002 0.000 HIS A 497 PHE 0.010 0.001 PHE A 432 TYR 0.018 0.001 TYR B 99 ARG 0.004 0.000 ARG I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 735) hydrogen bonds : angle 4.06432 ( 2121) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.60316 ( 8) covalent geometry : bond 0.00275 (13020) covalent geometry : angle 0.62472 (17756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.42 seconds wall clock time: 61 minutes 0.72 seconds (3660.72 seconds total)