Starting phenix.real_space_refine on Thu Sep 18 01:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_8454.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_8454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_8454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_8454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_8454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tr1_8454/09_2025/5tr1_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 6 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: 6 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.36, per 1000 atoms: 0.27 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: 0.84 Conformation dependent library (CDL) restraints added in 594.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.48 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: 2.44 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1928 1.31 - 1.44: 3739 1.44 - 1.56: 7217 1.56 - 1.69: 30 1.69 - 1.81: 106 Bond restraints: 13020 Sorted by residual: bond pdb=" CA ILE B 123 " pdb=" CB ILE B 123 " ideal model delta sigma weight residual 1.537 1.564 -0.027 5.00e-03 4.00e+04 2.96e+01 bond pdb=" CA ILE A 123 " pdb=" CB ILE A 123 " ideal model delta sigma weight residual 1.537 1.563 -0.027 5.00e-03 4.00e+04 2.83e+01 bond pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" CA SER B 296 " pdb=" C SER B 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C SER B 64 " pdb=" O SER B 64 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.89e+01 ... (remaining 13015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 13698 1.75 - 3.50: 3543 3.50 - 5.25: 387 5.25 - 7.00: 104 7.00 - 8.75: 24 Bond angle restraints: 17756 Sorted by residual: angle pdb=" O ILE B 123 " pdb=" C ILE B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 120.42 125.59 -5.17 6.40e-01 2.44e+00 6.54e+01 angle pdb=" O ILE A 123 " pdb=" C ILE A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 120.42 125.54 -5.12 6.40e-01 2.44e+00 6.40e+01 angle pdb=" O LEU A 499 " pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 120.27 125.77 -5.50 6.90e-01 2.10e+00 6.35e+01 angle pdb=" O LEU B 499 " pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 120.27 125.72 -5.45 6.90e-01 2.10e+00 6.24e+01 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 111.11 119.86 -8.75 1.20e+00 6.94e-01 5.32e+01 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 6954 16.49 - 32.97: 552 32.97 - 49.46: 120 49.46 - 65.95: 32 65.95 - 82.43: 2 Dihedral angle restraints: 7660 sinusoidal: 2908 harmonic: 4752 Sorted by residual: dihedral pdb=" C THR B 417 " pdb=" N THR B 417 " pdb=" CA THR B 417 " pdb=" CB THR B 417 " ideal model delta harmonic sigma weight residual -122.00 -138.55 16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C THR A 417 " pdb=" N THR A 417 " pdb=" CA THR A 417 " pdb=" CB THR A 417 " ideal model delta harmonic sigma weight residual -122.00 -138.47 16.47 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" C VAL B 174 " pdb=" N VAL B 174 " pdb=" CA VAL B 174 " pdb=" CB VAL B 174 " ideal model delta harmonic sigma weight residual -122.00 -136.99 14.99 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1770 0.123 - 0.247: 224 0.247 - 0.370: 38 0.370 - 0.494: 22 0.494 - 0.617: 2 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA THR B 417 " pdb=" N THR B 417 " pdb=" C THR B 417 " pdb=" CB THR B 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA THR A 417 " pdb=" N THR A 417 " pdb=" C THR A 417 " pdb=" CB THR A 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2053 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 618 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 618 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU A 618 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN A 619 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 618 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU B 618 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU B 618 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 619 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 166 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C VAL B 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY B 167 " -0.018 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 77 2.67 - 3.22: 12159 3.22 - 3.78: 20041 3.78 - 4.34: 25676 4.34 - 4.90: 43062 Nonbonded interactions: 101015 Sorted by model distance: nonbonded pdb=" O ALA B 471 " pdb=" OG SER B 475 " model vdw 2.107 3.040 nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 475 " model vdw 2.107 3.040 nonbonded pdb=" O ALA B 368 " pdb=" OG1 THR B 371 " model vdw 2.363 3.040 nonbonded pdb=" O ALA A 368 " pdb=" OG1 THR A 371 " model vdw 2.364 3.040 nonbonded pdb=" O ILE A 398 " pdb=" OG1 THR A 401 " model vdw 2.401 3.040 ... (remaining 101010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 13024 Z= 0.588 Angle : 1.542 8.754 17764 Z= 1.163 Chirality : 0.095 0.617 2056 Planarity : 0.006 0.057 2188 Dihedral : 12.777 82.433 4592 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 2.23 % Allowed : 7.22 % Favored : 90.55 % Cbeta Deviations : 2.88 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00821 (13020) covalent geometry : angle 1.54234 (17756) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.97728 ( 8) hydrogen bonds : bond 0.14474 ( 735) hydrogen bonds : angle 5.43324 ( 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 : 0.500 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: 0.1205 time to fit residues: 51.7766 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 : 0.487 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 313 ASN A 564 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035086 restraints weight = 88741.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.036196 restraints weight = 45215.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036933 restraints weight = 28090.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.037500 restraints weight = 20341.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.037925 restraints weight = 15423.705| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2522 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= 0.144 Angle : 0.652 7.245 17764 Z= 0.330 Chirality : 0.042 0.267 2056 Planarity : 0.005 0.049 2188 Dihedral : 6.288 54.421 1898 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.31 % Allowed : 14.29 % Favored : 83.41 % 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 aren not related in a simple way. whole: 1.62 (0.22), residues: 1620 helix: 3.56 (0.18), residues: 826 sheet: -0.95 (0.34), residues: 182 loop : -2.00 (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 B 99 PHE 0.015 0.001 PHE I 79 TRP 0.011 0.001 TRP B 234 HIS 0.004 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00321 (13020) covalent geometry : angle 0.65207 (17756) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.65169 ( 8) hydrogen bonds : bond 0.04424 ( 735) hydrogen bonds : angle 4.46658 ( 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 192 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.450 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: 0.8929 (mmm) cc_final: 0.8534 (mmm) REVERT: A 64 SER cc_start: 0.9239 (t) cc_final: 0.8934 (p) REVERT: A 212 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (m) REVERT: A 354 MET cc_start: 0.8938 (mmt) cc_final: 0.8721 (tpt) REVERT: A 363 ASP cc_start: 0.8153 (t0) cc_final: 0.7909 (t0) REVERT: A 412 MET cc_start: 0.9258 (mtp) cc_final: 0.8468 (mtp) REVERT: A 421 MET cc_start: 0.7871 (ptm) cc_final: 0.7299 (ttp) REVERT: H 101 ASP cc_start: 0.7734 (m-30) cc_final: 0.6672 (m-30) REVERT: L 27 GLN cc_start: 0.8671 (mt0) cc_final: 0.8386 (mt0) REVERT: L 55 TYR cc_start: 0.7839 (t80) cc_final: 0.6998 (t80) REVERT: L 89 GLN cc_start: 0.8748 (tt0) cc_final: 0.8272 (tm-30) REVERT: L 96 LEU cc_start: 0.9418 (mt) cc_final: 0.9218 (mt) REVERT: L 106 LEU cc_start: 0.8390 (tt) cc_final: 0.7914 (tt) REVERT: B 60 MET cc_start: 0.8935 (mmm) cc_final: 0.8547 (mmm) REVERT: B 64 SER cc_start: 0.9331 (t) cc_final: 0.8992 (p) REVERT: B 212 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8501 (m) REVERT: B 354 MET cc_start: 0.8960 (mmt) cc_final: 0.8741 (tpt) REVERT: B 412 MET cc_start: 0.9252 (mtp) cc_final: 0.8473 (mtp) REVERT: B 421 MET cc_start: 0.7865 (ptm) cc_final: 0.7305 (ttp) REVERT: I 101 ASP cc_start: 0.7731 (m-30) cc_final: 0.6680 (m-30) REVERT: M 55 TYR cc_start: 0.7858 (t80) cc_final: 0.7054 (t80) REVERT: M 89 GLN cc_start: 0.8731 (tt0) cc_final: 0.8317 (tm-30) outliers start: 31 outliers final: 16 residues processed: 184 average time/residue: 0.1056 time to fit residues: 28.6073 Evaluate side-chains 129 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 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 436 ILE 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: 0.6980 chunk 71 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 497 HIS H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 497 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.039713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.033616 restraints weight = 89791.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.034679 restraints weight = 45567.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.035460 restraints weight = 28293.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.035940 restraints weight = 20283.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036371 restraints weight = 15546.094| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13024 Z= 0.169 Angle : 0.626 6.314 17764 Z= 0.318 Chirality : 0.041 0.202 2056 Planarity : 0.005 0.048 2188 Dihedral : 5.260 46.416 1886 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.24 % Allowed : 15.10 % Favored : 80.65 % 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 aren not related in a simple way. whole: 1.49 (0.22), residues: 1620 helix: 3.30 (0.18), residues: 830 sheet: -1.30 (0.32), residues: 216 loop : -1.74 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 553 TYR 0.023 0.002 TYR I 33 PHE 0.011 0.002 PHE A 550 TRP 0.023 0.002 TRP A 411 HIS 0.004 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00382 (13020) covalent geometry : angle 0.62549 (17756) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.77726 ( 8) hydrogen bonds : bond 0.04010 ( 735) hydrogen bonds : angle 4.30213 ( 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 187 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9037 (mmm) cc_final: 0.8663 (mmm) REVERT: A 64 SER cc_start: 0.9354 (t) cc_final: 0.9065 (p) REVERT: A 180 LEU cc_start: 0.9513 (mm) cc_final: 0.8995 (tt) REVERT: A 212 VAL cc_start: 0.8587 (p) cc_final: 0.8297 (m) REVERT: A 354 MET cc_start: 0.8896 (mmt) cc_final: 0.8344 (tpp) REVERT: A 359 ASP cc_start: 0.8953 (m-30) cc_final: 0.8666 (m-30) REVERT: A 421 MET cc_start: 0.7964 (ptm) cc_final: 0.6950 (ttm) REVERT: H 49 MET cc_start: 0.9082 (mmm) cc_final: 0.8642 (mtt) REVERT: H 101 ASP cc_start: 0.8057 (m-30) cc_final: 0.7336 (m-30) REVERT: L 52 SER cc_start: 0.8909 (t) cc_final: 0.8705 (p) REVERT: L 55 TYR cc_start: 0.7768 (t80) cc_final: 0.7052 (t80) REVERT: L 106 LEU cc_start: 0.8412 (tt) cc_final: 0.8145 (tt) REVERT: L 107 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.5824 (mmmt) REVERT: B 60 MET cc_start: 0.9029 (mmm) cc_final: 0.8647 (mmm) REVERT: B 64 SER cc_start: 0.9322 (t) cc_final: 0.9024 (p) REVERT: B 212 VAL cc_start: 0.8569 (p) cc_final: 0.8276 (m) REVERT: B 354 MET cc_start: 0.8891 (mmt) cc_final: 0.8491 (tpp) REVERT: B 355 ARG cc_start: 0.8802 (ptt180) cc_final: 0.8595 (ptm160) REVERT: B 359 ASP cc_start: 0.8962 (m-30) cc_final: 0.8657 (m-30) REVERT: B 421 MET cc_start: 0.7932 (ptm) cc_final: 0.6977 (ttm) REVERT: B 503 MET cc_start: 0.9097 (mtm) cc_final: 0.8723 (mtm) REVERT: I 49 MET cc_start: 0.8625 (mmm) cc_final: 0.8334 (mmm) REVERT: I 101 ASP cc_start: 0.8045 (m-30) cc_final: 0.7341 (m-30) REVERT: M 55 TYR cc_start: 0.7854 (t80) cc_final: 0.7097 (t80) REVERT: M 89 GLN cc_start: 0.8810 (tt0) cc_final: 0.8580 (tt0) outliers start: 57 outliers final: 28 residues processed: 172 average time/residue: 0.1033 time to fit residues: 26.6767 Evaluate side-chains 138 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 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 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: 6.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 0.0060 chunk 160 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 32 ASN L 89 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.039166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.033217 restraints weight = 90394.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.034249 restraints weight = 46615.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034986 restraints weight = 29027.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.035553 restraints weight = 20870.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.035937 restraints weight = 15807.659| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13024 Z= 0.182 Angle : 0.599 6.370 17764 Z= 0.306 Chirality : 0.040 0.231 2056 Planarity : 0.004 0.033 2188 Dihedral : 5.419 56.691 1886 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.87 % Allowed : 14.06 % Favored : 82.07 % 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 aren not related in a simple way. whole: 1.31 (0.22), residues: 1620 helix: 2.98 (0.18), residues: 832 sheet: -1.15 (0.33), residues: 218 loop : -1.64 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.015 0.002 TYR I 33 PHE 0.010 0.002 PHE B 432 TRP 0.010 0.001 TRP I 48 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00405 (13020) covalent geometry : angle 0.59869 (17756) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.71249 ( 8) hydrogen bonds : bond 0.03994 ( 735) hydrogen bonds : angle 4.31846 ( 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 166 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9360 (t) cc_final: 0.9072 (p) REVERT: A 175 MET cc_start: 0.8921 (ttm) cc_final: 0.8156 (mtp) REVERT: A 212 VAL cc_start: 0.8480 (p) cc_final: 0.8197 (m) REVERT: A 354 MET cc_start: 0.8889 (mmt) cc_final: 0.8500 (tpp) REVERT: A 359 ASP cc_start: 0.8921 (m-30) cc_final: 0.8572 (m-30) REVERT: A 421 MET cc_start: 0.7886 (ptm) cc_final: 0.7280 (ttp) REVERT: H 33 TYR cc_start: 0.8365 (m-80) cc_final: 0.7990 (m-80) REVERT: H 38 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (tt) REVERT: H 49 MET cc_start: 0.9089 (mmm) cc_final: 0.8639 (mtt) REVERT: H 101 ASP cc_start: 0.8022 (m-30) cc_final: 0.7186 (m-30) REVERT: L 55 TYR cc_start: 0.7737 (t80) cc_final: 0.6969 (t80) REVERT: L 106 LEU cc_start: 0.8395 (tt) cc_final: 0.8171 (tt) REVERT: L 107 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.5320 (tptp) REVERT: B 64 SER cc_start: 0.9363 (t) cc_final: 0.9081 (p) REVERT: B 175 MET cc_start: 0.8922 (ttm) cc_final: 0.8244 (mtp) REVERT: B 354 MET cc_start: 0.8915 (mmt) cc_final: 0.8508 (tpp) REVERT: B 355 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8543 (ptm160) REVERT: B 359 ASP cc_start: 0.8946 (m-30) cc_final: 0.8585 (m-30) REVERT: B 421 MET cc_start: 0.7878 (ptm) cc_final: 0.7294 (ttp) REVERT: I 33 TYR cc_start: 0.8351 (m-80) cc_final: 0.7994 (m-80) REVERT: I 45 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8429 (mmtt) REVERT: I 49 MET cc_start: 0.8670 (mmm) cc_final: 0.8456 (mmm) REVERT: I 101 ASP cc_start: 0.8182 (m-30) cc_final: 0.7338 (m-30) REVERT: M 55 TYR cc_start: 0.7825 (t80) cc_final: 0.7104 (t80) outliers start: 52 outliers final: 42 residues processed: 151 average time/residue: 0.1022 time to fit residues: 23.6110 Evaluate side-chains 141 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 604 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 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 L residue 107 LYS 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 486 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 I residue 109 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 chunk 146 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.039440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.033588 restraints weight = 90175.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.034644 restraints weight = 46649.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035348 restraints weight = 29070.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.035868 restraints weight = 21058.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036291 restraints weight = 16132.007| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13024 Z= 0.141 Angle : 0.570 8.758 17764 Z= 0.288 Chirality : 0.039 0.226 2056 Planarity : 0.004 0.034 2188 Dihedral : 5.237 55.905 1886 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.79 % Allowed : 14.36 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.21), residues: 1620 helix: 3.04 (0.18), residues: 816 sheet: -1.01 (0.34), residues: 218 loop : -1.45 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.013 0.001 TYR B 99 PHE 0.012 0.001 PHE L 98 TRP 0.010 0.001 TRP I 48 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00320 (13020) covalent geometry : angle 0.57044 (17756) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.57427 ( 8) hydrogen bonds : bond 0.03731 ( 735) hydrogen bonds : angle 4.19688 ( 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 170 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9173 (mmm) cc_final: 0.8915 (mmm) REVERT: A 64 SER cc_start: 0.9364 (t) cc_final: 0.9077 (p) REVERT: A 175 MET cc_start: 0.8921 (ttm) cc_final: 0.8201 (mtp) REVERT: A 212 VAL cc_start: 0.8481 (p) cc_final: 0.8190 (m) REVERT: A 354 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8526 (tpp) REVERT: A 359 ASP cc_start: 0.8930 (m-30) cc_final: 0.8529 (m-30) REVERT: A 421 MET cc_start: 0.7922 (ptm) cc_final: 0.7415 (ttp) REVERT: H 38 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8736 (tt) REVERT: H 49 MET cc_start: 0.8946 (mmm) cc_final: 0.8606 (mtt) REVERT: H 101 ASP cc_start: 0.7999 (m-30) cc_final: 0.6973 (m-30) REVERT: L 55 TYR cc_start: 0.7686 (t80) cc_final: 0.6890 (t80) REVERT: B 60 MET cc_start: 0.9167 (mmm) cc_final: 0.8908 (mmm) REVERT: B 64 SER cc_start: 0.9367 (t) cc_final: 0.9086 (p) REVERT: B 175 MET cc_start: 0.8889 (ttm) cc_final: 0.8233 (mtp) REVERT: B 212 VAL cc_start: 0.8456 (p) cc_final: 0.8184 (m) REVERT: B 354 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8529 (tpp) REVERT: B 355 ARG cc_start: 0.8820 (ptt180) cc_final: 0.8581 (ptm160) REVERT: B 359 ASP cc_start: 0.8928 (m-30) cc_final: 0.8482 (m-30) REVERT: B 421 MET cc_start: 0.7862 (ptm) cc_final: 0.7269 (ttp) REVERT: I 101 ASP cc_start: 0.7895 (m-30) cc_final: 0.6892 (m-30) REVERT: M 55 TYR cc_start: 0.7723 (t80) cc_final: 0.6881 (t80) outliers start: 51 outliers final: 35 residues processed: 157 average time/residue: 0.1077 time to fit residues: 25.2077 Evaluate side-chains 136 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain 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 350 SER Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 2 ILE 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: 4.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN I 3 GLN I 5 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032559 restraints weight = 92498.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033568 restraints weight = 47633.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.034277 restraints weight = 29745.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.034657 restraints weight = 21483.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035166 restraints weight = 17118.741| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13024 Z= 0.230 Angle : 0.643 10.097 17764 Z= 0.329 Chirality : 0.040 0.213 2056 Planarity : 0.005 0.036 2188 Dihedral : 5.505 57.224 1886 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.46 % Allowed : 14.29 % Favored : 81.25 % 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 aren not related in a simple way. whole: 1.17 (0.21), residues: 1620 helix: 2.69 (0.18), residues: 816 sheet: -0.94 (0.34), residues: 216 loop : -1.40 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 355 TYR 0.019 0.002 TYR I 33 PHE 0.012 0.002 PHE I 80 TRP 0.027 0.002 TRP I 48 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00505 (13020) covalent geometry : angle 0.64328 (17756) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.73577 ( 8) hydrogen bonds : bond 0.04192 ( 735) hydrogen bonds : angle 4.40468 ( 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: 60 poor density : 101 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9398 (t) cc_final: 0.9128 (p) REVERT: A 175 MET cc_start: 0.8932 (ttm) cc_final: 0.8206 (mtp) REVERT: A 359 ASP cc_start: 0.8916 (m-30) cc_final: 0.8515 (m-30) REVERT: A 396 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: A 421 MET cc_start: 0.7796 (ptm) cc_final: 0.7083 (ttp) REVERT: H 38 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8840 (tt) REVERT: H 101 ASP cc_start: 0.8082 (m-30) cc_final: 0.7324 (m-30) REVERT: L 55 TYR cc_start: 0.7843 (t80) cc_final: 0.7232 (t80) REVERT: L 107 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.5659 (tptp) REVERT: B 64 SER cc_start: 0.9376 (t) cc_final: 0.9097 (p) REVERT: B 175 MET cc_start: 0.8829 (ttm) cc_final: 0.8174 (mtp) REVERT: B 355 ARG cc_start: 0.8799 (ptt180) cc_final: 0.8545 (ptm160) REVERT: B 359 ASP cc_start: 0.8901 (m-30) cc_final: 0.8511 (m-30) REVERT: B 396 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: B 421 MET cc_start: 0.7880 (ptm) cc_final: 0.7105 (ttp) REVERT: I 49 MET cc_start: 0.8597 (mmm) cc_final: 0.8319 (mmt) REVERT: I 101 ASP cc_start: 0.8247 (m-30) cc_final: 0.7457 (m-30) REVERT: M 55 TYR cc_start: 0.7879 (t80) cc_final: 0.7261 (t80) outliers start: 60 outliers final: 41 residues processed: 143 average time/residue: 0.1005 time to fit residues: 21.8069 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 H residue 38 ILE 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 L residue 107 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 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 396 PHE 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 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 2 ILE 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: 7.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 141 optimal weight: 0.0970 chunk 159 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033754 restraints weight = 90758.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034791 restraints weight = 46840.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.035527 restraints weight = 29208.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.036092 restraints weight = 21172.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036531 restraints weight = 16088.798| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13024 Z= 0.126 Angle : 0.573 8.656 17764 Z= 0.286 Chirality : 0.038 0.222 2056 Planarity : 0.004 0.036 2188 Dihedral : 5.193 55.365 1886 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.68 % Allowed : 15.77 % Favored : 81.55 % 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 aren not related in a simple way. whole: 1.34 (0.21), residues: 1620 helix: 2.87 (0.18), residues: 812 sheet: -0.76 (0.35), residues: 218 loop : -1.39 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 39 TYR 0.015 0.001 TYR B 99 PHE 0.010 0.001 PHE A 432 TRP 0.019 0.001 TRP I 48 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00286 (13020) covalent geometry : angle 0.57273 (17756) SS BOND : bond 0.00361 ( 4) SS BOND : angle 0.67308 ( 8) hydrogen bonds : bond 0.03681 ( 735) hydrogen bonds : angle 4.19658 ( 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 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9397 (t) cc_final: 0.9108 (p) REVERT: A 175 MET cc_start: 0.8906 (ttm) cc_final: 0.8209 (mtp) REVERT: A 212 VAL cc_start: 0.8474 (p) cc_final: 0.8208 (m) REVERT: A 359 ASP cc_start: 0.8847 (m-30) cc_final: 0.8412 (m-30) REVERT: A 396 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: A 412 MET cc_start: 0.9315 (mtt) cc_final: 0.8881 (mtt) REVERT: A 421 MET cc_start: 0.7902 (ptm) cc_final: 0.7268 (ttp) REVERT: A 440 LEU cc_start: 0.9231 (mm) cc_final: 0.9010 (tt) REVERT: H 101 ASP cc_start: 0.8152 (m-30) cc_final: 0.7326 (m-30) REVERT: L 55 TYR cc_start: 0.7768 (t80) cc_final: 0.7389 (t80) REVERT: L 104 LEU cc_start: 0.8413 (tp) cc_final: 0.8100 (tt) REVERT: B 64 SER cc_start: 0.9398 (t) cc_final: 0.9112 (p) REVERT: B 175 MET cc_start: 0.8879 (ttm) cc_final: 0.8186 (mtp) REVERT: B 212 VAL cc_start: 0.8443 (p) cc_final: 0.8192 (m) REVERT: B 348 MET cc_start: 0.9119 (ttt) cc_final: 0.8574 (tpp) REVERT: B 396 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: B 421 MET cc_start: 0.7911 (ptm) cc_final: 0.7260 (ttp) REVERT: B 440 LEU cc_start: 0.9228 (mm) cc_final: 0.9005 (tt) REVERT: I 49 MET cc_start: 0.8326 (mmm) cc_final: 0.8046 (mmt) REVERT: I 101 ASP cc_start: 0.8151 (m-30) cc_final: 0.7397 (m-30) REVERT: M 55 TYR cc_start: 0.7774 (t80) cc_final: 0.7409 (t80) REVERT: M 104 LEU cc_start: 0.8388 (tp) cc_final: 0.8074 (tt) outliers start: 36 outliers final: 25 residues processed: 136 average time/residue: 0.0979 time to fit residues: 20.1286 Evaluate side-chains 122 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 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 415 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 396 PHE 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 100 VAL 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: 0.2980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.034095 restraints weight = 90391.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.035141 restraints weight = 46773.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035835 restraints weight = 29320.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036423 restraints weight = 21400.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.036874 restraints weight = 16179.507| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13024 Z= 0.119 Angle : 0.581 10.134 17764 Z= 0.284 Chirality : 0.038 0.220 2056 Planarity : 0.004 0.036 2188 Dihedral : 5.005 54.286 1886 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.60 % Allowed : 15.77 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.21), residues: 1620 helix: 2.84 (0.18), residues: 812 sheet: -0.58 (0.35), residues: 218 loop : -1.37 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.016 0.001 TYR A 99 PHE 0.008 0.001 PHE A 432 TRP 0.017 0.001 TRP I 48 HIS 0.002 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00276 (13020) covalent geometry : angle 0.58079 (17756) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.76270 ( 8) hydrogen bonds : bond 0.03539 ( 735) hydrogen bonds : angle 4.10928 ( 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 152 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9371 (t) cc_final: 0.9074 (p) REVERT: A 175 MET cc_start: 0.8914 (ttm) cc_final: 0.8069 (mtp) REVERT: A 212 VAL cc_start: 0.8408 (p) cc_final: 0.8159 (m) REVERT: A 348 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8574 (tpp) REVERT: A 359 ASP cc_start: 0.8917 (m-30) cc_final: 0.8448 (m-30) REVERT: A 396 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7773 (m-10) REVERT: A 412 MET cc_start: 0.9333 (mtt) cc_final: 0.8887 (mtm) REVERT: A 421 MET cc_start: 0.7921 (ptm) cc_final: 0.7348 (ttp) REVERT: A 576 MET cc_start: 0.7548 (ppp) cc_final: 0.7266 (ppp) REVERT: H 44 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8846 (mmtt) REVERT: H 45 LYS cc_start: 0.8944 (ptpp) cc_final: 0.8435 (mmtt) REVERT: H 101 ASP cc_start: 0.8239 (m-30) cc_final: 0.7440 (m-30) REVERT: L 55 TYR cc_start: 0.7678 (t80) cc_final: 0.7279 (t80) REVERT: B 64 SER cc_start: 0.9369 (t) cc_final: 0.9055 (p) REVERT: B 175 MET cc_start: 0.8873 (ttm) cc_final: 0.8145 (mtp) REVERT: B 212 VAL cc_start: 0.8470 (p) cc_final: 0.8214 (m) REVERT: B 348 MET cc_start: 0.9106 (ttt) cc_final: 0.8707 (tpp) REVERT: B 359 ASP cc_start: 0.8867 (m-30) cc_final: 0.8449 (m-30) REVERT: B 396 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 411 TRP cc_start: 0.8435 (t60) cc_final: 0.8143 (t60) REVERT: B 421 MET cc_start: 0.7963 (ptm) cc_final: 0.7400 (ttp) REVERT: B 503 MET cc_start: 0.9031 (mtp) cc_final: 0.8708 (mtm) REVERT: I 45 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8303 (mtmm) REVERT: I 49 MET cc_start: 0.8406 (mmm) cc_final: 0.8148 (mmt) REVERT: I 101 ASP cc_start: 0.8071 (m-30) cc_final: 0.7321 (m-30) REVERT: M 55 TYR cc_start: 0.7681 (t80) cc_final: 0.7302 (t80) REVERT: M 89 GLN cc_start: 0.8622 (tt0) cc_final: 0.7781 (tm-30) outliers start: 35 outliers final: 22 residues processed: 142 average time/residue: 0.0992 time to fit residues: 21.4714 Evaluate side-chains 128 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 396 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.040597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034656 restraints weight = 88507.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.035663 restraints weight = 45781.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.036520 restraints weight = 29110.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.037009 restraints weight = 20329.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.037370 restraints weight = 15810.763| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13024 Z= 0.106 Angle : 0.581 8.797 17764 Z= 0.281 Chirality : 0.039 0.216 2056 Planarity : 0.004 0.035 2188 Dihedral : 4.857 52.554 1886 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.86 % Allowed : 17.04 % Favored : 81.10 % 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 aren not related in a simple way. whole: 1.44 (0.21), residues: 1620 helix: 2.80 (0.18), residues: 816 sheet: -0.23 (0.37), residues: 198 loop : -1.30 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 39 TYR 0.017 0.001 TYR B 99 PHE 0.008 0.001 PHE L 98 TRP 0.019 0.001 TRP H 48 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00240 (13020) covalent geometry : angle 0.58142 (17756) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.74069 ( 8) hydrogen bonds : bond 0.03390 ( 735) hydrogen bonds : angle 4.06577 ( 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 141 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9348 (t) cc_final: 0.9043 (p) REVERT: A 175 MET cc_start: 0.8930 (ttm) cc_final: 0.8069 (mtp) REVERT: A 180 LEU cc_start: 0.9481 (mm) cc_final: 0.8987 (tt) REVERT: A 212 VAL cc_start: 0.8324 (p) cc_final: 0.8084 (m) REVERT: A 359 ASP cc_start: 0.8936 (m-30) cc_final: 0.8448 (m-30) REVERT: A 363 ASP cc_start: 0.7730 (t0) cc_final: 0.7508 (t0) REVERT: A 396 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: A 412 MET cc_start: 0.9244 (mtt) cc_final: 0.8991 (mtt) REVERT: A 421 MET cc_start: 0.8073 (ptm) cc_final: 0.7525 (ttp) REVERT: A 462 MET cc_start: 0.8162 (tpt) cc_final: 0.7949 (mmm) REVERT: A 576 MET cc_start: 0.7534 (ppp) cc_final: 0.7300 (ppp) REVERT: H 44 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8908 (mmtt) REVERT: H 45 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8417 (mmtt) REVERT: H 49 MET cc_start: 0.8556 (mtt) cc_final: 0.7854 (mpp) REVERT: H 101 ASP cc_start: 0.8107 (m-30) cc_final: 0.7401 (m-30) REVERT: L 55 TYR cc_start: 0.7939 (t80) cc_final: 0.7333 (t80) REVERT: B 64 SER cc_start: 0.9352 (t) cc_final: 0.9031 (p) REVERT: B 175 MET cc_start: 0.8883 (ttm) cc_final: 0.8195 (mtp) REVERT: B 212 VAL cc_start: 0.8342 (p) cc_final: 0.8093 (m) REVERT: B 348 MET cc_start: 0.9165 (ttt) cc_final: 0.8746 (tpp) REVERT: B 359 ASP cc_start: 0.8886 (m-30) cc_final: 0.8416 (m-30) REVERT: B 363 ASP cc_start: 0.7787 (t0) cc_final: 0.7555 (t0) REVERT: B 396 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7824 (m-10) REVERT: B 411 TRP cc_start: 0.8459 (t60) cc_final: 0.8163 (t60) REVERT: B 421 MET cc_start: 0.8009 (ptm) cc_final: 0.7409 (ttp) REVERT: B 462 MET cc_start: 0.8190 (tpt) cc_final: 0.7886 (mmm) REVERT: I 45 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8318 (mtmm) REVERT: I 49 MET cc_start: 0.8344 (mmm) cc_final: 0.8094 (mmt) REVERT: I 101 ASP cc_start: 0.8078 (m-30) cc_final: 0.7351 (m-30) REVERT: M 4 MET cc_start: 0.7858 (mmm) cc_final: 0.7328 (mmm) REVERT: M 55 TYR cc_start: 0.7852 (t80) cc_final: 0.7250 (t80) REVERT: M 89 GLN cc_start: 0.8613 (tt0) cc_final: 0.7865 (tm-30) outliers start: 25 outliers final: 18 residues processed: 134 average time/residue: 0.0842 time to fit residues: 18.1771 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 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 396 PHE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 543 HIS ** 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 = 0.2833 r_free = 0.2833 target = 0.039419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.033392 restraints weight = 92623.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.034477 restraints weight = 47982.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035211 restraints weight = 30011.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.035758 restraints weight = 21713.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036212 restraints weight = 16506.627| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13024 Z= 0.168 Angle : 0.609 8.716 17764 Z= 0.300 Chirality : 0.039 0.220 2056 Planarity : 0.004 0.035 2188 Dihedral : 4.933 52.499 1886 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.79 % Allowed : 17.11 % Favored : 81.10 % 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 aren not related in a simple way. whole: 1.40 (0.21), residues: 1620 helix: 2.78 (0.18), residues: 812 sheet: -0.48 (0.35), residues: 222 loop : -1.27 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.017 0.002 TYR A 99 PHE 0.009 0.001 PHE B 389 TRP 0.018 0.001 TRP H 48 HIS 0.037 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00378 (13020) covalent geometry : angle 0.60921 (17756) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.74971 ( 8) hydrogen bonds : bond 0.03705 ( 735) hydrogen bonds : angle 4.17122 ( 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 123 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9368 (t) cc_final: 0.9078 (p) REVERT: A 175 MET cc_start: 0.8865 (ttm) cc_final: 0.8031 (mtp) REVERT: A 348 MET cc_start: 0.9158 (ttt) cc_final: 0.8520 (tpp) REVERT: A 359 ASP cc_start: 0.8911 (m-30) cc_final: 0.8515 (m-30) REVERT: A 396 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7885 (m-10) REVERT: A 412 MET cc_start: 0.9281 (mtt) cc_final: 0.8912 (mtm) REVERT: A 421 MET cc_start: 0.8019 (ptm) cc_final: 0.7471 (ttp) REVERT: A 576 MET cc_start: 0.7550 (ppp) cc_final: 0.7255 (ppp) REVERT: H 101 ASP cc_start: 0.8231 (m-30) cc_final: 0.7621 (m-30) REVERT: L 55 TYR cc_start: 0.7877 (t80) cc_final: 0.7375 (t80) REVERT: B 64 SER cc_start: 0.9404 (t) cc_final: 0.9108 (p) REVERT: B 175 MET cc_start: 0.8841 (ttm) cc_final: 0.8148 (mtp) REVERT: B 359 ASP cc_start: 0.8913 (m-30) cc_final: 0.8520 (m-30) REVERT: B 396 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: B 411 TRP cc_start: 0.8485 (t60) cc_final: 0.8225 (t60) REVERT: B 421 MET cc_start: 0.7907 (ptm) cc_final: 0.7284 (ttp) REVERT: I 49 MET cc_start: 0.8311 (mmm) cc_final: 0.8098 (mmt) REVERT: I 101 ASP cc_start: 0.8052 (m-30) cc_final: 0.7481 (m-30) REVERT: M 55 TYR cc_start: 0.7830 (t80) cc_final: 0.7351 (t80) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.0852 time to fit residues: 16.3871 Evaluate side-chains 114 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 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 396 PHE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain M residue 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: 0.7980 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 7 optimal weight: 0.0030 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.034032 restraints weight = 91143.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.035101 restraints weight = 46756.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.035829 restraints weight = 29066.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.036404 restraints weight = 21135.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.036890 restraints weight = 16039.457| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13024 Z= 0.126 Angle : 0.617 10.469 17764 Z= 0.295 Chirality : 0.038 0.210 2056 Planarity : 0.004 0.036 2188 Dihedral : 4.836 50.680 1886 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 16.96 % Favored : 81.03 % 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 aren not related in a simple way. whole: 1.45 (0.21), residues: 1620 helix: 2.77 (0.18), residues: 812 sheet: -0.32 (0.36), residues: 218 loop : -1.21 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.016 0.001 TYR B 99 PHE 0.010 0.001 PHE I 79 TRP 0.020 0.001 TRP H 48 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00290 (13020) covalent geometry : angle 0.61715 (17756) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.73698 ( 8) hydrogen bonds : bond 0.03575 ( 735) hydrogen bonds : angle 4.12417 ( 2121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.24 seconds wall clock time: 30 minutes 42.99 seconds (1842.99 seconds total)