Starting phenix.real_space_refine on Sat Sep 12 01:38:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.cif" model { file = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2026/5tr1_8454.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 2} 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: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 2} 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: 4 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 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: 4 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.62, per 1000 atoms: 0.21 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: 0.76 Conformation dependent library (CDL) restraints added in 473.0 milliseconds 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: 0.38 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: 1.91 Time building geometry restraints manager: 1.02 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: 6846 16.49 - 32.97: 548 32.97 - 49.46: 120 49.46 - 65.95: 32 65.95 - 82.43: 2 Dihedral angle restraints: 7548 sinusoidal: 2796 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 7545 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 : 12.849 82.433 4480 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG I 98 TYR 0.026 0.002 TYR B 357 PHE 0.023 0.003 PHE B 410 TRP 0.028 0.003 TRP A 50 HIS 0.006 0.002 HIS B 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.59 (13020) covalent geometry : angle 1.54234 / 1.16 (17756) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 0.97728 / 0.48 ( 8) hydrogen bonds : bond 0.14474 / 10.14 ( 735) hydrogen bonds : angle 5.43324 / 4.10 ( 2121) *********************** 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 : 0.372 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: 0.8628 (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: 0.8562 (ptm-80) 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: 0.9082 (mmm) REVERT: I 67 ARG cc_start: 0.8960 (ptp-170) cc_final: 0.8530 (ptm-80) 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: 0.1075 time to fit residues: 47.2063 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN A 313 ASN A 564 GLN H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 313 ASN B 564 GLN I 3 GLN I 5 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.041406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035130 restraints weight = 88669.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.036203 restraints weight = 45251.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.037001 restraints weight = 28025.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037444 restraints weight = 20128.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.037947 restraints weight = 15766.436| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13024 Z= 0.142 Angle : 0.645 7.316 17764 Z= 0.326 Chirality : 0.041 0.254 2056 Planarity : 0.005 0.051 2188 Dihedral : 5.761 51.274 1786 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.38 % Allowed : 14.06 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1620 helix: 3.52 (0.18), residues: 826 sheet: -0.91 (0.34), residues: 182 loop : -1.98 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 595 TYR 0.020 0.002 TYR A 99 PHE 0.017 0.001 PHE H 79 TRP 0.008 0.001 TRP B 234 HIS 0.003 0.001 HIS B 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13020) covalent geometry : angle 0.64528 / 0.33 (17756) SS BOND : bond 0.00151 / 0.08 ( 4) SS BOND : angle 0.69615 / 0.31 ( 8) hydrogen bonds : bond 0.04394 / 2.96 ( 735) hydrogen bonds : angle 4.44570 / 3.35 ( 2121) *********************** 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 196 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.413 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: A 60 MET cc_start: 0.8928 (mmm) cc_final: 0.8534 (mmm) REVERT: A 64 SER cc_start: 0.9355 (t) cc_final: 0.9012 (p) REVERT: A 212 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (m) REVERT: A 354 MET cc_start: 0.8942 (mmt) cc_final: 0.8723 (tpt) REVERT: A 363 ASP cc_start: 0.8153 (t0) cc_final: 0.7901 (t0) REVERT: A 408 MET cc_start: 0.8953 (mmm) cc_final: 0.8693 (mmm) REVERT: A 412 MET cc_start: 0.9259 (mtp) cc_final: 0.8444 (mtp) REVERT: A 421 MET cc_start: 0.7874 (ptm) cc_final: 0.7315 (ttp) REVERT: H 101 ASP cc_start: 0.7738 (m-30) cc_final: 0.6690 (m-30) REVERT: L 27 GLN cc_start: 0.8672 (mt0) cc_final: 0.8397 (mt0) REVERT: L 55 TYR cc_start: 0.7864 (t80) cc_final: 0.7020 (t80) REVERT: L 89 GLN cc_start: 0.8732 (tt0) cc_final: 0.8173 (tm-30) REVERT: L 106 LEU cc_start: 0.8396 (tt) cc_final: 0.8010 (tt) REVERT: B 60 MET cc_start: 0.8934 (mmm) cc_final: 0.8548 (mmm) REVERT: B 64 SER cc_start: 0.9348 (t) cc_final: 0.9011 (p) REVERT: B 212 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8488 (m) REVERT: B 354 MET cc_start: 0.8962 (mmt) cc_final: 0.8742 (tpt) REVERT: B 408 MET cc_start: 0.8946 (mmm) cc_final: 0.8678 (mmm) REVERT: B 412 MET cc_start: 0.9250 (mtp) cc_final: 0.8430 (mtp) REVERT: B 421 MET cc_start: 0.7871 (ptm) cc_final: 0.7322 (ttp) REVERT: I 101 ASP cc_start: 0.7734 (m-30) cc_final: 0.6685 (m-30) REVERT: M 27 GLN cc_start: 0.8692 (mt0) cc_final: 0.8394 (mt0) REVERT: M 55 TYR cc_start: 0.7869 (t80) cc_final: 0.7008 (t80) REVERT: M 89 GLN cc_start: 0.8741 (tt0) cc_final: 0.8185 (tm-30) outliers start: 32 outliers final: 14 residues processed: 188 average time/residue: 0.1060 time to fit residues: 29.5193 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 461 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 461 ILE Chi-restraints excluded: chain I residue 3 GLN 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 15 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN A 497 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.040222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.034133 restraints weight = 88807.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.035180 restraints weight = 45776.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.035935 restraints weight = 28654.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.036447 restraints weight = 20759.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036863 restraints weight = 15864.999| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13024 Z= 0.145 Angle : 0.606 5.994 17764 Z= 0.307 Chirality : 0.041 0.218 2056 Planarity : 0.004 0.048 2188 Dihedral : 4.805 31.648 1774 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.17 % Allowed : 13.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1620 helix: 3.39 (0.18), residues: 832 sheet: -1.05 (0.34), residues: 196 loop : -1.75 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 182 TYR 0.022 0.001 TYR H 33 PHE 0.012 0.001 PHE B 550 TRP 0.021 0.001 TRP B 411 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13020) covalent geometry : angle 0.60614 / 0.31 (17756) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 0.71712 / 0.33 ( 8) hydrogen bonds : bond 0.03878 / 2.62 ( 735) hydrogen bonds : angle 4.22119 / 3.16 ( 2121) *********************** 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 185 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9029 (mmm) cc_final: 0.8655 (mmm) REVERT: A 64 SER cc_start: 0.9346 (t) cc_final: 0.9050 (p) REVERT: A 180 LEU cc_start: 0.9502 (mm) cc_final: 0.8969 (tt) REVERT: A 212 VAL cc_start: 0.8592 (p) cc_final: 0.8302 (m) REVERT: A 354 MET cc_start: 0.8855 (mmt) cc_final: 0.8471 (tpp) REVERT: A 359 ASP cc_start: 0.8940 (m-30) cc_final: 0.8662 (m-30) REVERT: A 421 MET cc_start: 0.7924 (ptm) cc_final: 0.6902 (ttm) REVERT: A 538 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7139 (ptm-80) REVERT: H 49 MET cc_start: 0.9051 (mmm) cc_final: 0.8562 (mtt) REVERT: H 101 ASP cc_start: 0.8024 (m-30) cc_final: 0.7276 (m-30) REVERT: L 55 TYR cc_start: 0.7680 (t80) cc_final: 0.6979 (t80) REVERT: L 89 GLN cc_start: 0.8705 (tt0) cc_final: 0.8468 (tt0) REVERT: B 60 MET cc_start: 0.9014 (mmm) cc_final: 0.8626 (mmm) REVERT: B 64 SER cc_start: 0.9368 (t) cc_final: 0.9049 (p) REVERT: B 212 VAL cc_start: 0.8574 (p) cc_final: 0.8281 (m) REVERT: B 320 MET cc_start: 0.9035 (tpp) cc_final: 0.8829 (tpp) REVERT: B 354 MET cc_start: 0.8883 (mmt) cc_final: 0.8485 (tpp) REVERT: B 359 ASP cc_start: 0.8810 (m-30) cc_final: 0.8509 (m-30) REVERT: B 421 MET cc_start: 0.7902 (ptm) cc_final: 0.6924 (ttm) REVERT: B 503 MET cc_start: 0.9070 (mtm) cc_final: 0.8866 (mtm) REVERT: B 538 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7138 (ptm-80) REVERT: I 101 ASP cc_start: 0.8003 (m-30) cc_final: 0.7269 (m-30) REVERT: M 55 TYR cc_start: 0.7761 (t80) cc_final: 0.7032 (t80) REVERT: M 89 GLN cc_start: 0.8738 (tt0) cc_final: 0.8481 (tt0) outliers start: 56 outliers final: 27 residues processed: 170 average time/residue: 0.1037 time to fit residues: 26.6323 Evaluate side-chains 141 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL 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 461 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 B residue 67 MET Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 286 VAL 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 461 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 159 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 147 optimal weight: 0.0060 chunk 160 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 386 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN 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 = 0.039419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.033407 restraints weight = 89579.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.034500 restraints weight = 45637.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.035218 restraints weight = 28285.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.035794 restraints weight = 20401.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.036190 restraints weight = 15244.848| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13024 Z= 0.168 Angle : 0.588 6.349 17764 Z= 0.301 Chirality : 0.040 0.225 2056 Planarity : 0.004 0.044 2188 Dihedral : 4.692 28.266 1774 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.57 % Allowed : 13.99 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1620 helix: 3.03 (0.18), residues: 836 sheet: -1.02 (0.34), residues: 216 loop : -1.64 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 182 TYR 0.014 0.002 TYR H 33 PHE 0.010 0.001 PHE A 432 TRP 0.010 0.001 TRP I 48 HIS 0.004 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (13020) covalent geometry : angle 0.58845 / 0.30 (17756) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 0.66470 / 0.32 ( 8) hydrogen bonds : bond 0.03892 / 2.63 ( 735) hydrogen bonds : angle 4.23452 / 3.16 ( 2121) *********************** 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: 48 poor density : 119 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9357 (t) cc_final: 0.9064 (p) REVERT: A 175 MET cc_start: 0.8953 (ttm) cc_final: 0.8222 (mtp) REVERT: A 212 VAL cc_start: 0.8457 (p) cc_final: 0.8169 (m) REVERT: A 354 MET cc_start: 0.8900 (mmt) cc_final: 0.8533 (tpp) REVERT: A 359 ASP cc_start: 0.8919 (m-30) cc_final: 0.8583 (m-30) REVERT: A 421 MET cc_start: 0.7977 (ptm) cc_final: 0.7397 (ttp) REVERT: A 538 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7310 (ptm-80) REVERT: H 49 MET cc_start: 0.9011 (mmm) cc_final: 0.8647 (mtt) REVERT: H 101 ASP cc_start: 0.7951 (m-30) cc_final: 0.7072 (m-30) REVERT: L 55 TYR cc_start: 0.7804 (t80) cc_final: 0.7015 (t80) REVERT: L 89 GLN cc_start: 0.8714 (tt0) cc_final: 0.8443 (tt0) REVERT: B 64 SER cc_start: 0.9327 (t) cc_final: 0.9027 (p) REVERT: B 175 MET cc_start: 0.8930 (ttm) cc_final: 0.8214 (mtp) REVERT: B 180 LEU cc_start: 0.9480 (mm) cc_final: 0.8981 (tt) REVERT: B 354 MET cc_start: 0.8897 (mmt) cc_final: 0.8535 (tpp) REVERT: B 359 ASP cc_start: 0.8778 (m-30) cc_final: 0.8442 (m-30) REVERT: B 421 MET cc_start: 0.7871 (ptm) cc_final: 0.7252 (ttp) REVERT: B 503 MET cc_start: 0.9062 (mtm) cc_final: 0.8828 (mtm) REVERT: B 538 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7320 (ptm-80) REVERT: I 45 LYS cc_start: 0.8957 (ptpp) cc_final: 0.8613 (mtmm) REVERT: I 82 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7670 (tp-100) REVERT: I 101 ASP cc_start: 0.7916 (m-30) cc_final: 0.7076 (m-30) REVERT: M 55 TYR cc_start: 0.7844 (t80) cc_final: 0.7062 (t80) REVERT: M 89 GLN cc_start: 0.8719 (tt0) cc_final: 0.8449 (tt0) outliers start: 48 outliers final: 34 residues processed: 153 average time/residue: 0.0937 time to fit residues: 21.8804 Evaluate side-chains 137 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 230 HIS 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 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 538 ARG 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 233 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 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 46 THR 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 126 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033611 restraints weight = 90888.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.034676 restraints weight = 46638.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.035451 restraints weight = 29012.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036047 restraints weight = 20742.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.036489 restraints weight = 15574.307| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13024 Z= 0.139 Angle : 0.568 6.132 17764 Z= 0.285 Chirality : 0.038 0.221 2056 Planarity : 0.004 0.034 2188 Dihedral : 4.472 26.325 1774 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.50 % Allowed : 14.81 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1620 helix: 2.97 (0.18), residues: 832 sheet: -0.89 (0.34), residues: 216 loop : -1.60 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.012 0.001 TYR H 33 PHE 0.010 0.001 PHE A 432 TRP 0.012 0.001 TRP I 48 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13020) covalent geometry : angle 0.56768 / 0.28 (17756) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.58875 / 0.24 ( 8) hydrogen bonds : bond 0.03655 / 2.47 ( 735) hydrogen bonds : angle 4.14385 / 3.09 ( 2121) *********************** 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 169 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.318 Fit side-chains REVERT: A 60 MET cc_start: 0.9178 (mmm) cc_final: 0.8930 (mmm) REVERT: A 64 SER cc_start: 0.9360 (t) cc_final: 0.9071 (p) REVERT: A 175 MET cc_start: 0.8928 (ttm) cc_final: 0.8160 (mtp) REVERT: A 212 VAL cc_start: 0.8434 (p) cc_final: 0.8162 (m) REVERT: A 354 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: A 359 ASP cc_start: 0.8931 (m-30) cc_final: 0.8502 (m-30) REVERT: A 421 MET cc_start: 0.7962 (ptm) cc_final: 0.7406 (ttp) REVERT: A 538 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7335 (ptm-80) REVERT: H 33 TYR cc_start: 0.8398 (m-80) cc_final: 0.7961 (m-80) REVERT: H 45 LYS cc_start: 0.8926 (ptpp) cc_final: 0.8628 (mtmm) REVERT: H 49 MET cc_start: 0.8895 (mmm) cc_final: 0.8615 (mtt) REVERT: H 101 ASP cc_start: 0.8025 (m-30) cc_final: 0.7003 (m-30) REVERT: L 55 TYR cc_start: 0.7738 (t80) cc_final: 0.6884 (t80) REVERT: L 89 GLN cc_start: 0.8621 (tt0) cc_final: 0.8126 (tm-30) REVERT: B 60 MET cc_start: 0.9173 (mmm) cc_final: 0.8908 (mmm) REVERT: B 64 SER cc_start: 0.9355 (t) cc_final: 0.9070 (p) REVERT: B 175 MET cc_start: 0.8929 (ttm) cc_final: 0.8190 (mtp) REVERT: B 212 VAL cc_start: 0.8427 (p) cc_final: 0.8154 (m) REVERT: B 354 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8545 (tpp) REVERT: B 359 ASP cc_start: 0.8939 (m-30) cc_final: 0.8494 (m-30) REVERT: B 421 MET cc_start: 0.7939 (ptm) cc_final: 0.7417 (ttp) REVERT: B 503 MET cc_start: 0.9089 (mtm) cc_final: 0.8866 (mtm) REVERT: B 538 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7323 (ptm-80) REVERT: I 3 GLN cc_start: 0.8404 (tp40) cc_final: 0.7995 (tm-30) REVERT: I 33 TYR cc_start: 0.8433 (m-80) cc_final: 0.8018 (m-80) REVERT: I 45 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8576 (mtmm) REVERT: I 82 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7883 (tp-100) REVERT: I 101 ASP cc_start: 0.8012 (m-30) cc_final: 0.6997 (m-30) REVERT: M 55 TYR cc_start: 0.7790 (t80) cc_final: 0.6901 (t80) REVERT: M 89 GLN cc_start: 0.8741 (tt0) cc_final: 0.8249 (tm-30) outliers start: 47 outliers final: 29 residues processed: 154 average time/residue: 0.0955 time to fit residues: 22.2263 Evaluate side-chains 137 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 538 ARG 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 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 233 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 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 538 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.032876 restraints weight = 92567.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033874 restraints weight = 47861.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034638 restraints weight = 29823.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.035154 restraints weight = 21487.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035621 restraints weight = 16495.072| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4333 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= 0.204 Angle : 0.607 8.926 17764 Z= 0.308 Chirality : 0.039 0.203 2056 Planarity : 0.004 0.037 2188 Dihedral : 4.619 28.320 1774 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.17 % Allowed : 14.14 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1620 helix: 2.91 (0.18), residues: 814 sheet: -0.92 (0.34), residues: 216 loop : -1.43 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.014 0.002 TYR H 33 PHE 0.011 0.002 PHE B 432 TRP 0.027 0.002 TRP I 48 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (13020) covalent geometry : angle 0.60721 / 0.31 (17756) SS BOND : bond 0.00186 / 0.09 ( 4) SS BOND : angle 0.51061 / 0.24 ( 8) hydrogen bonds : bond 0.03950 / 2.69 ( 735) hydrogen bonds : angle 4.26347 / 3.16 ( 2121) *********************** 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 161 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9385 (t) cc_final: 0.9109 (p) REVERT: A 175 MET cc_start: 0.8916 (ttm) cc_final: 0.8178 (mtp) REVERT: A 348 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8628 (tpp) REVERT: A 354 MET cc_start: 0.8932 (mmt) cc_final: 0.8395 (tpp) REVERT: A 359 ASP cc_start: 0.8910 (m-30) cc_final: 0.8503 (m-30) REVERT: A 396 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: A 421 MET cc_start: 0.7809 (ptm) cc_final: 0.7286 (ttp) REVERT: A 538 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: H 49 MET cc_start: 0.8831 (mmm) cc_final: 0.8570 (mtt) REVERT: H 101 ASP cc_start: 0.8068 (m-30) cc_final: 0.7281 (m-30) REVERT: L 55 TYR cc_start: 0.7836 (t80) cc_final: 0.7296 (t80) REVERT: L 89 GLN cc_start: 0.8725 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 64 SER cc_start: 0.9359 (t) cc_final: 0.9069 (p) REVERT: B 175 MET cc_start: 0.8912 (ttm) cc_final: 0.8237 (mtp) REVERT: B 348 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8564 (tpp) REVERT: B 354 MET cc_start: 0.8927 (mmt) cc_final: 0.8528 (tpp) REVERT: B 359 ASP cc_start: 0.8866 (m-30) cc_final: 0.8480 (m-30) REVERT: B 396 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: B 412 MET cc_start: 0.9364 (mtt) cc_final: 0.9066 (mmt) REVERT: B 421 MET cc_start: 0.7807 (ptm) cc_final: 0.7241 (ttp) REVERT: B 538 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (ttt180) REVERT: I 3 GLN cc_start: 0.8426 (tp40) cc_final: 0.8025 (tm-30) REVERT: I 101 ASP cc_start: 0.8038 (m-30) cc_final: 0.7268 (m-30) REVERT: M 55 TYR cc_start: 0.7844 (t80) cc_final: 0.7314 (t80) REVERT: M 89 GLN cc_start: 0.8729 (tt0) cc_final: 0.8059 (tm-30) outliers start: 56 outliers final: 41 residues processed: 145 average time/residue: 0.0997 time to fit residues: 21.9306 Evaluate side-chains 138 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 348 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 538 ARG 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 H residue 109 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 49 TYR 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 233 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 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 436 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 538 ARG 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 46 THR 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 126 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.039607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.033592 restraints weight = 90956.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.034685 restraints weight = 46437.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.035358 restraints weight = 28819.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035971 restraints weight = 21005.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036422 restraints weight = 15848.829| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13024 Z= 0.139 Angle : 0.578 9.005 17764 Z= 0.286 Chirality : 0.038 0.216 2056 Planarity : 0.004 0.037 2188 Dihedral : 4.426 27.316 1774 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.83 % Allowed : 14.96 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1620 helix: 2.96 (0.18), residues: 816 sheet: -0.76 (0.35), residues: 216 loop : -1.43 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.014 0.001 TYR A 99 PHE 0.010 0.001 PHE B 432 TRP 0.023 0.001 TRP I 48 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13020) covalent geometry : angle 0.57827 / 0.29 (17756) SS BOND : bond 0.00149 / 0.08 ( 4) SS BOND : angle 0.60472 / 0.24 ( 8) hydrogen bonds : bond 0.03632 / 2.46 ( 735) hydrogen bonds : angle 4.14316 / 3.08 ( 2121) *********************** 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 147 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9385 (t) cc_final: 0.9091 (p) REVERT: A 175 MET cc_start: 0.8908 (ttm) cc_final: 0.8214 (mtp) REVERT: A 212 VAL cc_start: 0.8422 (p) cc_final: 0.8173 (m) REVERT: A 348 MET cc_start: 0.9171 (ttt) cc_final: 0.8704 (tpp) REVERT: A 354 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: A 359 ASP cc_start: 0.8903 (m-30) cc_final: 0.8437 (m-30) REVERT: A 396 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7816 (m-10) REVERT: A 412 MET cc_start: 0.9406 (mtt) cc_final: 0.9063 (mtt) REVERT: A 421 MET cc_start: 0.7994 (ptm) cc_final: 0.7445 (ttp) REVERT: A 440 LEU cc_start: 0.9227 (mm) cc_final: 0.9002 (tt) REVERT: H 101 ASP cc_start: 0.8273 (m-30) cc_final: 0.7516 (m-30) REVERT: L 55 TYR cc_start: 0.7876 (t80) cc_final: 0.7456 (t80) REVERT: L 89 GLN cc_start: 0.8728 (tt0) cc_final: 0.7976 (tm-30) REVERT: B 64 SER cc_start: 0.9386 (t) cc_final: 0.9095 (p) REVERT: B 175 MET cc_start: 0.8900 (ttm) cc_final: 0.8217 (mtp) REVERT: B 212 VAL cc_start: 0.8441 (p) cc_final: 0.8188 (m) REVERT: B 348 MET cc_start: 0.9167 (ttt) cc_final: 0.8618 (tpp) REVERT: B 354 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: B 359 ASP cc_start: 0.8862 (m-30) cc_final: 0.8420 (m-30) REVERT: B 396 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: B 421 MET cc_start: 0.7905 (ptm) cc_final: 0.7293 (ttp) REVERT: B 440 LEU cc_start: 0.9228 (mm) cc_final: 0.8999 (tt) REVERT: B 503 MET cc_start: 0.9114 (mtm) cc_final: 0.8758 (mtp) REVERT: I 3 GLN cc_start: 0.8503 (tp40) cc_final: 0.8113 (tm-30) REVERT: I 47 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6213 (tm-30) REVERT: I 49 MET cc_start: 0.7964 (mmm) cc_final: 0.7507 (mmm) REVERT: I 101 ASP cc_start: 0.8047 (m-30) cc_final: 0.7291 (m-30) REVERT: M 55 TYR cc_start: 0.7858 (t80) cc_final: 0.7430 (t80) REVERT: M 89 GLN cc_start: 0.8752 (tt0) cc_final: 0.8062 (tm-30) REVERT: M 104 LEU cc_start: 0.8387 (tp) cc_final: 0.8097 (tt) outliers start: 38 outliers final: 29 residues processed: 137 average time/residue: 0.1024 time to fit residues: 21.4153 Evaluate side-chains 130 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 96 CYS 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 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 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 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2852 r_free = 0.2852 target = 0.039948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033872 restraints weight = 90950.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034950 restraints weight = 46986.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.035711 restraints weight = 29328.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036167 restraints weight = 21169.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.036696 restraints weight = 16481.282| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13024 Z= 0.115 Angle : 0.575 8.458 17764 Z= 0.281 Chirality : 0.038 0.225 2056 Planarity : 0.004 0.036 2188 Dihedral : 4.341 26.525 1774 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.83 % Allowed : 14.81 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1620 helix: 2.94 (0.18), residues: 816 sheet: -0.60 (0.35), residues: 216 loop : -1.41 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.015 0.001 TYR A 99 PHE 0.008 0.001 PHE B 432 TRP 0.018 0.001 TRP I 48 HIS 0.002 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (13020) covalent geometry : angle 0.57520 / 0.28 (17756) SS BOND : bond 0.00176 / 0.09 ( 4) SS BOND : angle 0.65553 / 0.27 ( 8) hydrogen bonds : bond 0.03492 / 2.35 ( 735) hydrogen bonds : angle 4.07495 / 3.03 ( 2121) *********************** 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 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9382 (t) cc_final: 0.9079 (p) REVERT: A 175 MET cc_start: 0.8881 (ttm) cc_final: 0.8216 (mtp) REVERT: A 212 VAL cc_start: 0.8417 (p) cc_final: 0.8152 (m) REVERT: A 354 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: A 359 ASP cc_start: 0.8910 (m-30) cc_final: 0.8415 (m-30) REVERT: A 363 ASP cc_start: 0.7901 (t0) cc_final: 0.7691 (t0) REVERT: A 396 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: A 412 MET cc_start: 0.9378 (mtt) cc_final: 0.9028 (mtt) REVERT: A 421 MET cc_start: 0.8001 (ptm) cc_final: 0.7422 (ttp) REVERT: H 3 GLN cc_start: 0.8228 (tp40) cc_final: 0.7932 (tm-30) REVERT: H 101 ASP cc_start: 0.8260 (m-30) cc_final: 0.7487 (m-30) REVERT: L 55 TYR cc_start: 0.7774 (t80) cc_final: 0.7371 (t80) REVERT: L 89 GLN cc_start: 0.8751 (tt0) cc_final: 0.8033 (tm-30) REVERT: B 64 SER cc_start: 0.9356 (t) cc_final: 0.9044 (p) REVERT: B 175 MET cc_start: 0.8874 (ttm) cc_final: 0.8174 (mtp) REVERT: B 212 VAL cc_start: 0.8399 (p) cc_final: 0.8151 (m) REVERT: B 348 MET cc_start: 0.9170 (ttt) cc_final: 0.8549 (tpp) REVERT: B 354 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8585 (tpp) REVERT: B 359 ASP cc_start: 0.8902 (m-30) cc_final: 0.8404 (m-30) REVERT: B 363 ASP cc_start: 0.7903 (t0) cc_final: 0.7695 (t0) REVERT: B 396 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: B 412 MET cc_start: 0.9372 (mtt) cc_final: 0.9124 (mmt) REVERT: B 421 MET cc_start: 0.7880 (ptm) cc_final: 0.7202 (ttp) REVERT: B 503 MET cc_start: 0.9129 (mtm) cc_final: 0.8773 (mtp) REVERT: I 3 GLN cc_start: 0.8513 (tp40) cc_final: 0.8133 (tm-30) REVERT: I 47 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6149 (tm-30) REVERT: I 49 MET cc_start: 0.8175 (mmm) cc_final: 0.7765 (mmm) REVERT: I 101 ASP cc_start: 0.8114 (m-30) cc_final: 0.7322 (m-30) REVERT: M 55 TYR cc_start: 0.7754 (t80) cc_final: 0.7338 (t80) REVERT: M 89 GLN cc_start: 0.8738 (tt0) cc_final: 0.8082 (tm-30) outliers start: 38 outliers final: 28 residues processed: 144 average time/residue: 0.0934 time to fit residues: 20.8398 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE 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 33 VAL Chi-restraints excluded: chain L residue 49 TYR 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 233 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 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 M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 543 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.039971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.033963 restraints weight = 90041.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.035036 restraints weight = 46401.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.035763 restraints weight = 28980.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036305 restraints weight = 20945.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036728 restraints weight = 16018.488| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13024 Z= 0.118 Angle : 0.601 8.847 17764 Z= 0.288 Chirality : 0.038 0.218 2056 Planarity : 0.004 0.036 2188 Dihedral : 4.277 25.970 1774 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 14.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1620 helix: 2.89 (0.18), residues: 818 sheet: -0.47 (0.36), residues: 218 loop : -1.41 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 39 TYR 0.015 0.001 TYR A 99 PHE 0.012 0.001 PHE I 79 TRP 0.017 0.001 TRP I 48 HIS 0.022 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13020) covalent geometry : angle 0.60095 / 0.29 (17756) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.63226 / 0.27 ( 8) hydrogen bonds : bond 0.03438 / 2.32 ( 735) hydrogen bonds : angle 4.03822 / 3.01 ( 2121) *********************** 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: 39 poor density : 104 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9354 (t) cc_final: 0.9032 (p) REVERT: A 175 MET cc_start: 0.8944 (ttm) cc_final: 0.8248 (mtp) REVERT: A 212 VAL cc_start: 0.8363 (p) cc_final: 0.8112 (m) REVERT: A 354 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8618 (tpp) REVERT: A 359 ASP cc_start: 0.8907 (m-30) cc_final: 0.8407 (m-30) REVERT: A 363 ASP cc_start: 0.7833 (t0) cc_final: 0.7630 (t0) REVERT: A 396 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: A 412 MET cc_start: 0.9355 (mtt) cc_final: 0.8999 (mtt) REVERT: A 421 MET cc_start: 0.8049 (ptm) cc_final: 0.7442 (ttp) REVERT: A 576 MET cc_start: 0.7292 (ppp) cc_final: 0.7090 (ppp) REVERT: H 101 ASP cc_start: 0.8078 (m-30) cc_final: 0.7356 (m-30) REVERT: L 55 TYR cc_start: 0.7753 (t80) cc_final: 0.7289 (t80) REVERT: L 89 GLN cc_start: 0.8742 (tt0) cc_final: 0.8062 (tm-30) REVERT: B 64 SER cc_start: 0.9355 (t) cc_final: 0.9035 (p) REVERT: B 175 MET cc_start: 0.8936 (ttm) cc_final: 0.8224 (mtp) REVERT: B 348 MET cc_start: 0.9152 (ttt) cc_final: 0.8537 (tpp) REVERT: B 354 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8583 (tpp) REVERT: B 359 ASP cc_start: 0.8905 (m-30) cc_final: 0.8405 (m-30) REVERT: B 396 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: B 412 MET cc_start: 0.9361 (mtt) cc_final: 0.9116 (mmt) REVERT: B 421 MET cc_start: 0.8052 (ptm) cc_final: 0.7434 (ttp) REVERT: B 503 MET cc_start: 0.9134 (mtm) cc_final: 0.8834 (mtp) REVERT: I 3 GLN cc_start: 0.8518 (tp40) cc_final: 0.8127 (tm-30) REVERT: I 47 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6092 (tm-30) REVERT: I 49 MET cc_start: 0.8151 (mmm) cc_final: 0.7692 (mmm) REVERT: I 101 ASP cc_start: 0.8112 (m-30) cc_final: 0.7410 (m-30) REVERT: M 55 TYR cc_start: 0.7708 (t80) cc_final: 0.7326 (t80) REVERT: M 89 GLN cc_start: 0.8741 (tt0) cc_final: 0.8043 (tm-30) outliers start: 39 outliers final: 30 residues processed: 132 average time/residue: 0.0933 time to fit residues: 19.5853 Evaluate side-chains 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 3 GLN 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 33 VAL Chi-restraints excluded: chain L residue 49 TYR 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 233 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 HIS H 3 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032929 restraints weight = 92807.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.033980 restraints weight = 47471.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034734 restraints weight = 29449.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.035281 restraints weight = 21107.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035723 restraints weight = 16078.079| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13024 Z= 0.196 Angle : 0.640 8.805 17764 Z= 0.315 Chirality : 0.039 0.213 2056 Planarity : 0.004 0.037 2188 Dihedral : 4.482 27.870 1774 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.83 % Allowed : 14.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1620 helix: 2.86 (0.18), residues: 812 sheet: -0.55 (0.36), residues: 218 loop : -1.37 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 538 TYR 0.012 0.002 TYR H 33 PHE 0.011 0.001 PHE B 432 TRP 0.022 0.002 TRP I 48 HIS 0.003 0.001 HIS A 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (13020) covalent geometry : angle 0.63963 / 0.31 (17756) SS BOND : bond 0.00188 / 0.09 ( 4) SS BOND : angle 0.66762 / 0.31 ( 8) hydrogen bonds : bond 0.03810 / 2.59 ( 735) hydrogen bonds : angle 4.18154 / 3.10 ( 2121) ********************** 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 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.485 Fit side-chains REVERT: A 64 SER cc_start: 0.9382 (t) cc_final: 0.9087 (p) REVERT: A 175 MET cc_start: 0.8863 (ttm) cc_final: 0.8176 (mtp) REVERT: A 354 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8571 (tpp) REVERT: A 359 ASP cc_start: 0.8909 (m-30) cc_final: 0.8465 (m-30) REVERT: A 396 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: A 421 MET cc_start: 0.7808 (ptm) cc_final: 0.7214 (ttp) REVERT: A 576 MET cc_start: 0.7303 (ppp) cc_final: 0.6996 (ppp) REVERT: H 49 MET cc_start: 0.8673 (mtt) cc_final: 0.8087 (mpp) REVERT: H 101 ASP cc_start: 0.8230 (m-30) cc_final: 0.7629 (m-30) REVERT: L 55 TYR cc_start: 0.7851 (t80) cc_final: 0.7396 (t80) REVERT: L 89 GLN cc_start: 0.8798 (tt0) cc_final: 0.7961 (tm-30) REVERT: B 64 SER cc_start: 0.9401 (t) cc_final: 0.9106 (p) REVERT: B 175 MET cc_start: 0.8854 (ttm) cc_final: 0.8229 (mtp) REVERT: B 348 MET cc_start: 0.9184 (ttt) cc_final: 0.8636 (tpp) REVERT: B 354 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8572 (tpp) REVERT: B 359 ASP cc_start: 0.8907 (m-30) cc_final: 0.8462 (m-30) REVERT: B 396 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: B 421 MET cc_start: 0.7846 (ptm) cc_final: 0.6774 (ttm) REVERT: B 503 MET cc_start: 0.9101 (mtm) cc_final: 0.8703 (mtp) REVERT: I 3 GLN cc_start: 0.8503 (tp40) cc_final: 0.8128 (tm-30) REVERT: I 101 ASP cc_start: 0.8066 (m-30) cc_final: 0.7492 (m-30) REVERT: M 55 TYR cc_start: 0.7790 (t80) cc_final: 0.7353 (t80) REVERT: M 89 GLN cc_start: 0.8791 (tt0) cc_final: 0.7942 (tm-30) outliers start: 38 outliers final: 31 residues processed: 124 average time/residue: 0.1021 time to fit residues: 20.0580 Evaluate side-chains 127 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 658 VAL 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 33 VAL Chi-restraints excluded: chain L residue 49 TYR 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 233 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 408 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 658 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 7 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.040297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.034379 restraints weight = 89279.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.035446 restraints weight = 45884.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036163 restraints weight = 28410.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.036701 restraints weight = 20637.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037114 restraints weight = 16210.718| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13024 Z= 0.108 Angle : 0.609 9.997 17764 Z= 0.289 Chirality : 0.038 0.209 2056 Planarity : 0.004 0.036 2188 Dihedral : 4.243 25.268 1774 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.23 % Allowed : 15.62 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1620 helix: 2.87 (0.18), residues: 814 sheet: -0.30 (0.36), residues: 218 loop : -1.31 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.017 0.001 TYR B 99 PHE 0.010 0.001 PHE I 79 TRP 0.017 0.001 TRP I 48 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13020) covalent geometry : angle 0.60864 / 0.29 (17756) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.68595 / 0.27 ( 8) hydrogen bonds : bond 0.03401 / 2.28 ( 735) hydrogen bonds : angle 4.01705 / 2.99 ( 2121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.56 seconds wall clock time: 30 minutes 18.15 seconds (1818.15 seconds total)