Starting phenix.real_space_refine on Wed Jul 30 18:50:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.map" model { file = "/net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tqq_8435/07_2025/5tqq_8435.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 8190 2.51 5 N 2048 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4594 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 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: "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: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4594 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 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: "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 Time building chain proxies: 7.86, per 1000 atoms: 0.63 Number of scatterers: 12574 At special positions: 0 Unit cell: (102.7, 107.9, 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 64 16.00 O 2272 8.00 N 2048 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 56.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 49 through 86 removed outlier: 4.593A pdb=" N GLY A 86 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.529A pdb=" N ARG A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.506A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.765A pdb=" N LEU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.879A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.313A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 193 through 214 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.527A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 278 through 313 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 323 through 339 Processing helix chain 'A' and resid 340 through 349 removed outlier: 5.670A pdb=" N ARG A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.648A 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: 3.886A pdb=" N PHE A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 419 removed outlier: 3.517A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.835A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.801A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 4.537A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.862A pdb=" N PHE A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.590A pdb=" N VAL A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) 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 'L' and resid 79 through 83 removed outlier: 3.944A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.688A 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 'B' and resid 49 through 86 removed outlier: 4.593A pdb=" N GLY B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 3.530A pdb=" N ARG B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 3.506A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.765A pdb=" N LEU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.881A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.313A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 188 Processing helix chain 'B' and resid 193 through 214 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.525A pdb=" N GLY B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 221 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 Processing helix chain 'B' and resid 278 through 313 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 323 through 339 Processing helix chain 'B' and resid 340 through 349 removed outlier: 5.669A pdb=" N ARG B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.648A 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: 3.886A pdb=" N PHE B 389 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.517A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.835A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.802A pdb=" N LEU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 4.536A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.556A 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: 3.863A pdb=" N PHE B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.589A pdb=" N VAL B 567 " --> pdb=" O PRO B 563 " (cutoff:3.500A) 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 'M' and resid 79 through 83 removed outlier: 3.944A pdb=" N LEU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.689A 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 sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.654A pdb=" N LEU A 558 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 579 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A 593 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 581 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 669 removed outlier: 5.787A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 666 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 633 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 659 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 635 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 633 " --> pdb=" O PHE B 657 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR B 659 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 635 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 666 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.599A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.949A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.029A pdb=" N TRP L 50 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.534A pdb=" N GLN H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP H 73 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 558 through 559 removed outlier: 6.655A pdb=" N LEU B 558 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 579 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 593 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 581 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.598A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 10 through 13 removed outlier: 5.949A pdb=" N MET M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR M 102 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR M 86 " --> pdb=" O THR M 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 53 through 54 removed outlier: 4.029A pdb=" N TRP M 50 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.534A pdb=" N GLN I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP I 73 " --> pdb=" O GLN I 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR I 102 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2007 1.32 - 1.45: 3648 1.45 - 1.57: 7139 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 12906 Sorted by residual: bond pdb=" C PHE A 65 " pdb=" O PHE A 65 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.86e+01 bond pdb=" C PHE B 65 " pdb=" O PHE B 65 " ideal model delta sigma weight residual 1.236 1.286 -0.049 1.15e-02 7.56e+03 1.84e+01 bond pdb=" C GLN B 303 " pdb=" O GLN B 303 " ideal model delta sigma weight residual 1.236 1.282 -0.045 1.15e-02 7.56e+03 1.54e+01 bond pdb=" C GLN A 303 " pdb=" O GLN A 303 " ideal model delta sigma weight residual 1.236 1.282 -0.045 1.15e-02 7.56e+03 1.53e+01 bond pdb=" C GLY A 72 " pdb=" O GLY A 72 " ideal model delta sigma weight residual 1.234 1.273 -0.040 1.21e-02 6.83e+03 1.07e+01 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 13537 1.71 - 3.41: 3517 3.41 - 5.12: 432 5.12 - 6.82: 79 6.82 - 8.53: 27 Bond angle restraints: 17592 Sorted by residual: angle pdb=" O LEU B 499 " pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 120.27 125.66 -5.39 6.90e-01 2.10e+00 6.09e+01 angle pdb=" O LEU A 499 " pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 120.27 125.56 -5.29 6.90e-01 2.10e+00 5.87e+01 angle pdb=" N ILE B 525 " pdb=" CA ILE B 525 " pdb=" CB ILE B 525 " ideal model delta sigma weight residual 110.55 119.08 -8.53 1.17e+00 7.31e-01 5.32e+01 angle pdb=" N ILE A 525 " pdb=" CA ILE A 525 " pdb=" CB ILE A 525 " ideal model delta sigma weight residual 110.55 119.06 -8.51 1.17e+00 7.31e-01 5.29e+01 angle pdb=" N PRO B 341 " pdb=" CA PRO B 341 " pdb=" C PRO B 341 " ideal model delta sigma weight residual 110.70 119.06 -8.36 1.22e+00 6.72e-01 4.70e+01 ... (remaining 17587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.61: 6619 13.61 - 27.22: 685 27.22 - 40.83: 154 40.83 - 54.44: 42 54.44 - 68.04: 12 Dihedral angle restraints: 7512 sinusoidal: 2776 harmonic: 4736 Sorted by residual: dihedral pdb=" C ILE B 511 " pdb=" N ILE B 511 " pdb=" CA ILE B 511 " pdb=" CB ILE B 511 " ideal model delta harmonic sigma weight residual -122.00 -140.23 18.23 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" C ILE A 511 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta harmonic sigma weight residual -122.00 -140.16 18.16 0 2.50e+00 1.60e-01 5.28e+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 -137.75 15.75 0 2.50e+00 1.60e-01 3.97e+01 ... (remaining 7509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1763 0.122 - 0.243: 217 0.243 - 0.365: 38 0.365 - 0.486: 8 0.486 - 0.608: 6 Chirality restraints: 2032 Sorted by residual: chirality pdb=" CA ILE B 511 " pdb=" N ILE B 511 " pdb=" C ILE B 511 " pdb=" CB ILE B 511 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.61 2.00e-01 2.50e+01 9.24e+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 1.83 0.60 2.00e-01 2.50e+01 9.09e+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 1.94 0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 2029 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 101 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL B 101 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 101 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 102 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.37e+01 pdb=" C VAL A 101 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 412 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C MET B 412 " -0.063 2.00e-02 2.50e+03 pdb=" O MET B 412 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 413 " 0.022 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 124 2.69 - 3.24: 13047 3.24 - 3.79: 19495 3.79 - 4.35: 25730 4.35 - 4.90: 42283 Nonbonded interactions: 100679 Sorted by model distance: nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 475 " model vdw 2.136 3.040 nonbonded pdb=" O ALA B 471 " pdb=" OG SER B 475 " model vdw 2.137 3.040 nonbonded pdb=" O ALA A 368 " pdb=" OG1 THR A 371 " model vdw 2.360 3.040 nonbonded pdb=" O ALA B 368 " pdb=" OG1 THR B 371 " model vdw 2.361 3.040 nonbonded pdb=" O LEU B 335 " pdb=" OG1 THR B 339 " model vdw 2.395 3.040 ... (remaining 100674 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.550 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 0.056 12910 Z= 0.584 Angle : 1.517 8.531 17600 Z= 1.142 Chirality : 0.093 0.608 2032 Planarity : 0.006 0.082 2188 Dihedral : 12.216 68.044 4456 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 0.89 % Allowed : 5.36 % Favored : 93.75 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 1618 helix: 1.65 (0.14), residues: 794 sheet: -1.34 (0.36), residues: 172 loop : -2.17 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 411 HIS 0.009 0.002 HIS B 497 PHE 0.027 0.003 PHE A 410 TYR 0.022 0.002 TYR B 138 ARG 0.007 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.15807 ( 728) hydrogen bonds : angle 6.13555 ( 2172) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.29547 ( 8) covalent geometry : bond 0.00821 (12906) covalent geometry : angle 1.51705 (17592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 316 time to evaluate : 1.435 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 140 ASP cc_start: 0.8072 (t0) cc_final: 0.7651 (t70) REVERT: A 217 PHE cc_start: 0.8162 (m-80) cc_final: 0.7929 (m-80) REVERT: A 240 PHE cc_start: 0.8316 (t80) cc_final: 0.7950 (t80) REVERT: A 363 ASP cc_start: 0.7855 (t0) cc_final: 0.7620 (t0) REVERT: A 412 MET cc_start: 0.8739 (mtp) cc_final: 0.8518 (mtt) REVERT: A 551 MET cc_start: 0.9198 (ptm) cc_final: 0.8855 (ptt) REVERT: L 17 ASP cc_start: 0.8361 (m-30) cc_final: 0.8112 (m-30) REVERT: L 39 LYS cc_start: 0.9131 (mttt) cc_final: 0.8899 (mmmt) REVERT: L 55 TYR cc_start: 0.8558 (t80) cc_final: 0.7595 (t80) REVERT: L 61 ARG cc_start: 0.7784 (ptt90) cc_final: 0.7164 (ptt90) REVERT: L 77 ASN cc_start: 0.9339 (m-40) cc_final: 0.8954 (t0) REVERT: L 79 GLN cc_start: 0.9071 (mt0) cc_final: 0.8639 (mp10) REVERT: L 83 LEU cc_start: 0.8755 (mt) cc_final: 0.8528 (mm) REVERT: H 32 ASP cc_start: 0.8662 (t0) cc_final: 0.8057 (m-30) REVERT: H 33 TYR cc_start: 0.7983 (m-80) cc_final: 0.7739 (m-80) REVERT: H 47 GLU cc_start: 0.8585 (tt0) cc_final: 0.8074 (tt0) REVERT: H 49 MET cc_start: 0.8955 (mmm) cc_final: 0.8338 (mmm) REVERT: H 67 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8161 (mtm180) REVERT: H 82 GLN cc_start: 0.8919 (mt0) cc_final: 0.8558 (mp10) REVERT: H 101 ASP cc_start: 0.9081 (m-30) cc_final: 0.8848 (m-30) REVERT: B 140 ASP cc_start: 0.8069 (t0) cc_final: 0.7654 (t70) REVERT: B 217 PHE cc_start: 0.8193 (m-80) cc_final: 0.7925 (m-80) REVERT: B 240 PHE cc_start: 0.8313 (t80) cc_final: 0.7907 (t80) REVERT: B 359 ASP cc_start: 0.8834 (m-30) cc_final: 0.8608 (m-30) REVERT: B 363 ASP cc_start: 0.7855 (t0) cc_final: 0.7622 (t0) REVERT: B 412 MET cc_start: 0.8732 (mtp) cc_final: 0.8522 (mtt) REVERT: B 551 MET cc_start: 0.9190 (ptm) cc_final: 0.8854 (ptt) REVERT: M 17 ASP cc_start: 0.8359 (m-30) cc_final: 0.8110 (m-30) REVERT: M 39 LYS cc_start: 0.9128 (mttt) cc_final: 0.8901 (mmmt) REVERT: M 55 TYR cc_start: 0.8552 (t80) cc_final: 0.7499 (t80) REVERT: M 61 ARG cc_start: 0.7754 (ptt90) cc_final: 0.7138 (ptt90) REVERT: M 77 ASN cc_start: 0.9335 (m-40) cc_final: 0.8953 (t0) REVERT: M 79 GLN cc_start: 0.9067 (mt0) cc_final: 0.8642 (mp10) REVERT: M 83 LEU cc_start: 0.8768 (mt) cc_final: 0.8542 (mm) REVERT: I 32 ASP cc_start: 0.8660 (t0) cc_final: 0.8073 (m-30) REVERT: I 33 TYR cc_start: 0.8000 (m-80) cc_final: 0.7757 (m-80) REVERT: I 47 GLU cc_start: 0.8588 (tt0) cc_final: 0.8074 (tt0) REVERT: I 49 MET cc_start: 0.8946 (mmm) cc_final: 0.8336 (mmm) REVERT: I 67 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8166 (mtm180) REVERT: I 82 GLN cc_start: 0.8915 (mt0) cc_final: 0.8554 (mp10) REVERT: I 101 ASP cc_start: 0.9068 (m-30) cc_final: 0.8828 (m-30) outliers start: 12 outliers final: 2 residues processed: 320 average time/residue: 0.2549 time to fit residues: 116.6622 Evaluate side-chains 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0670 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 198 ASN A 386 ASN A 480 HIS L 32 ASN B 78 HIS B 198 ASN B 386 ASN B 480 HIS M 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.045355 restraints weight = 60313.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.046919 restraints weight = 27401.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.047958 restraints weight = 16119.699| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12910 Z= 0.138 Angle : 0.636 7.388 17600 Z= 0.319 Chirality : 0.041 0.163 2032 Planarity : 0.005 0.051 2188 Dihedral : 4.950 54.974 1752 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.71 % Allowed : 13.24 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1618 helix: 3.59 (0.18), residues: 812 sheet: -1.49 (0.33), residues: 210 loop : -1.55 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.004 0.001 HIS B 497 PHE 0.020 0.002 PHE B 52 TYR 0.013 0.002 TYR B 236 ARG 0.004 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 728) hydrogen bonds : angle 4.57311 ( 2172) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.57321 ( 8) covalent geometry : bond 0.00306 (12906) covalent geometry : angle 0.63603 (17592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.9208 (mtp) cc_final: 0.8980 (mtp) REVERT: A 240 PHE cc_start: 0.8574 (t80) cc_final: 0.8185 (t80) REVERT: A 353 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 354 MET cc_start: 0.9395 (mmm) cc_final: 0.9094 (mmt) REVERT: A 356 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 412 MET cc_start: 0.8746 (mtp) cc_final: 0.8508 (mtt) REVERT: A 503 MET cc_start: 0.8967 (ttm) cc_final: 0.8346 (mtm) REVERT: A 551 MET cc_start: 0.8469 (ptm) cc_final: 0.8100 (ptt) REVERT: L 4 MET cc_start: 0.7896 (mmm) cc_final: 0.7334 (mmm) REVERT: L 55 TYR cc_start: 0.8054 (t80) cc_final: 0.6959 (t80) REVERT: L 61 ARG cc_start: 0.7833 (ptt90) cc_final: 0.7276 (ptt90) REVERT: L 77 ASN cc_start: 0.8867 (m-40) cc_final: 0.8648 (t0) REVERT: H 32 ASP cc_start: 0.8406 (t0) cc_final: 0.7772 (m-30) REVERT: H 47 GLU cc_start: 0.8185 (tt0) cc_final: 0.7959 (tt0) REVERT: H 49 MET cc_start: 0.9068 (mmm) cc_final: 0.8748 (mmm) REVERT: H 101 ASP cc_start: 0.8405 (m-30) cc_final: 0.8089 (m-30) REVERT: B 175 MET cc_start: 0.9209 (mtp) cc_final: 0.8990 (mtp) REVERT: B 240 PHE cc_start: 0.8573 (t80) cc_final: 0.8187 (t80) REVERT: B 353 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 354 MET cc_start: 0.9400 (mmm) cc_final: 0.9100 (mmt) REVERT: B 356 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8615 (mt-10) REVERT: B 359 ASP cc_start: 0.8415 (m-30) cc_final: 0.8005 (m-30) REVERT: B 412 MET cc_start: 0.8746 (mtp) cc_final: 0.8521 (mtt) REVERT: B 503 MET cc_start: 0.8970 (ttm) cc_final: 0.8430 (mtm) REVERT: B 551 MET cc_start: 0.8476 (ptm) cc_final: 0.8109 (ptt) REVERT: M 4 MET cc_start: 0.7891 (mmm) cc_final: 0.7314 (mmm) REVERT: M 55 TYR cc_start: 0.8039 (t80) cc_final: 0.6927 (t80) REVERT: M 61 ARG cc_start: 0.7848 (ptt90) cc_final: 0.7316 (ptt90) REVERT: M 77 ASN cc_start: 0.8873 (m-40) cc_final: 0.8651 (t0) REVERT: I 32 ASP cc_start: 0.8428 (t0) cc_final: 0.7798 (m-30) REVERT: I 47 GLU cc_start: 0.8195 (tt0) cc_final: 0.7976 (tt0) REVERT: I 49 MET cc_start: 0.9062 (mmm) cc_final: 0.8737 (mmm) REVERT: I 101 ASP cc_start: 0.8381 (m-30) cc_final: 0.8052 (m-30) outliers start: 23 outliers final: 10 residues processed: 215 average time/residue: 0.2563 time to fit residues: 78.9683 Evaluate side-chains 159 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 549 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044150 restraints weight = 62223.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.045670 restraints weight = 28074.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046707 restraints weight = 16484.679| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12910 Z= 0.143 Angle : 0.580 6.245 17600 Z= 0.294 Chirality : 0.040 0.152 2032 Planarity : 0.005 0.046 2188 Dihedral : 4.661 50.542 1752 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.60 % Allowed : 14.88 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1618 helix: 3.36 (0.18), residues: 812 sheet: -1.27 (0.33), residues: 210 loop : -1.26 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 48 HIS 0.003 0.001 HIS A 171 PHE 0.016 0.002 PHE H 79 TYR 0.018 0.002 TYR I 33 ARG 0.002 0.000 ARG I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 728) hydrogen bonds : angle 4.28936 ( 2172) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.30083 ( 8) covalent geometry : bond 0.00336 (12906) covalent geometry : angle 0.57964 (17592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.9173 (mtp) cc_final: 0.8935 (mtp) REVERT: A 225 GLU cc_start: 0.8787 (tt0) cc_final: 0.8391 (mt-10) REVERT: A 240 PHE cc_start: 0.8614 (t80) cc_final: 0.8072 (t80) REVERT: A 353 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 356 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8426 (mt-10) REVERT: A 359 ASP cc_start: 0.8706 (t0) cc_final: 0.8466 (m-30) REVERT: A 408 MET cc_start: 0.9019 (mmp) cc_final: 0.8744 (mmp) REVERT: A 503 MET cc_start: 0.8972 (ttm) cc_final: 0.8667 (mtm) REVERT: A 551 MET cc_start: 0.8417 (ptm) cc_final: 0.8048 (ptt) REVERT: L 10 PHE cc_start: 0.9044 (m-10) cc_final: 0.8801 (m-80) REVERT: L 55 TYR cc_start: 0.8167 (t80) cc_final: 0.6548 (t80) REVERT: H 27 ASP cc_start: 0.7505 (t0) cc_final: 0.7053 (t0) REVERT: H 32 ASP cc_start: 0.8421 (t0) cc_final: 0.7828 (m-30) REVERT: H 33 TYR cc_start: 0.8440 (m-80) cc_final: 0.8196 (m-80) REVERT: H 49 MET cc_start: 0.9071 (mmm) cc_final: 0.8817 (mmm) REVERT: H 101 ASP cc_start: 0.8418 (m-30) cc_final: 0.7870 (m-30) REVERT: B 175 MET cc_start: 0.9164 (mtp) cc_final: 0.8884 (mtp) REVERT: B 225 GLU cc_start: 0.8870 (tt0) cc_final: 0.8552 (mt-10) REVERT: B 240 PHE cc_start: 0.8632 (t80) cc_final: 0.8100 (t80) REVERT: B 359 ASP cc_start: 0.8519 (m-30) cc_final: 0.8174 (m-30) REVERT: B 408 MET cc_start: 0.9024 (mmp) cc_final: 0.8760 (mmp) REVERT: B 427 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9061 (mmt) REVERT: B 503 MET cc_start: 0.8976 (ttm) cc_final: 0.8554 (mtm) REVERT: B 551 MET cc_start: 0.8441 (ptm) cc_final: 0.8086 (ptt) REVERT: M 10 PHE cc_start: 0.9032 (m-10) cc_final: 0.8776 (m-80) REVERT: M 55 TYR cc_start: 0.8183 (t80) cc_final: 0.6563 (t80) REVERT: I 27 ASP cc_start: 0.7499 (t0) cc_final: 0.7040 (t0) REVERT: I 32 ASP cc_start: 0.8431 (t0) cc_final: 0.7841 (m-30) REVERT: I 33 TYR cc_start: 0.8440 (m-80) cc_final: 0.8197 (m-80) REVERT: I 47 GLU cc_start: 0.8260 (tt0) cc_final: 0.8034 (tt0) REVERT: I 49 MET cc_start: 0.9074 (mmm) cc_final: 0.8825 (mmm) REVERT: I 101 ASP cc_start: 0.8387 (m-30) cc_final: 0.8029 (m-30) outliers start: 35 outliers final: 22 residues processed: 188 average time/residue: 0.2322 time to fit residues: 64.8142 Evaluate side-chains 164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 84 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 108 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 393 HIS H 82 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 393 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.043734 restraints weight = 61963.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.045213 restraints weight = 27914.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.046241 restraints weight = 16598.207| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12910 Z= 0.183 Angle : 0.585 6.933 17600 Z= 0.296 Chirality : 0.040 0.150 2032 Planarity : 0.005 0.038 2188 Dihedral : 4.657 43.731 1752 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.42 % Allowed : 16.52 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1618 helix: 2.92 (0.18), residues: 816 sheet: -1.22 (0.33), residues: 216 loop : -0.93 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 391 HIS 0.003 0.001 HIS A 393 PHE 0.020 0.002 PHE I 79 TYR 0.018 0.002 TYR B 236 ARG 0.003 0.000 ARG H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 728) hydrogen bonds : angle 4.35131 ( 2172) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.13090 ( 8) covalent geometry : bond 0.00419 (12906) covalent geometry : angle 0.58555 (17592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 1.438 Fit side-chains REVERT: A 175 MET cc_start: 0.9199 (mtp) cc_final: 0.8910 (mtp) REVERT: A 225 GLU cc_start: 0.8854 (tt0) cc_final: 0.8577 (tt0) REVERT: A 250 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: A 353 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.7944 (p) REVERT: A 356 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8584 (mt-10) REVERT: A 551 MET cc_start: 0.8432 (ptm) cc_final: 0.8057 (ptt) REVERT: A 594 MET cc_start: 0.7904 (mmm) cc_final: 0.7543 (mmm) REVERT: L 4 MET cc_start: 0.7536 (mmm) cc_final: 0.7303 (mmm) REVERT: H 27 ASP cc_start: 0.7499 (t0) cc_final: 0.6965 (t0) REVERT: H 33 TYR cc_start: 0.8590 (m-80) cc_final: 0.8380 (m-80) REVERT: H 49 MET cc_start: 0.8974 (mmm) cc_final: 0.8761 (mmm) REVERT: B 175 MET cc_start: 0.9206 (mtp) cc_final: 0.8926 (mtp) REVERT: B 225 GLU cc_start: 0.8857 (tt0) cc_final: 0.8458 (mt-10) REVERT: B 250 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: B 353 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8752 (p) REVERT: B 356 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8462 (mt-10) REVERT: B 359 ASP cc_start: 0.8664 (m-30) cc_final: 0.8300 (m-30) REVERT: B 551 MET cc_start: 0.8420 (ptm) cc_final: 0.8047 (ptt) REVERT: B 594 MET cc_start: 0.7884 (mmm) cc_final: 0.7531 (mmm) REVERT: M 4 MET cc_start: 0.7505 (mmm) cc_final: 0.7268 (mmm) REVERT: I 20 LEU cc_start: 0.9131 (mp) cc_final: 0.8880 (mt) REVERT: I 27 ASP cc_start: 0.7499 (t0) cc_final: 0.6964 (t0) REVERT: I 47 GLU cc_start: 0.8317 (tt0) cc_final: 0.8074 (tt0) REVERT: I 49 MET cc_start: 0.9045 (mmm) cc_final: 0.8777 (mmm) outliers start: 46 outliers final: 17 residues processed: 182 average time/residue: 0.2137 time to fit residues: 58.8550 Evaluate side-chains 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 0.0970 chunk 161 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN L 89 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.043606 restraints weight = 61511.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.045102 restraints weight = 27980.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.046168 restraints weight = 16721.809| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12910 Z= 0.151 Angle : 0.569 6.346 17600 Z= 0.288 Chirality : 0.039 0.157 2032 Planarity : 0.004 0.044 2188 Dihedral : 4.539 43.974 1752 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.23 % Allowed : 17.78 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1618 helix: 2.87 (0.18), residues: 814 sheet: -1.07 (0.33), residues: 216 loop : -0.74 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.003 0.001 HIS A 230 PHE 0.023 0.002 PHE A 213 TYR 0.026 0.002 TYR I 33 ARG 0.011 0.001 ARG M 18 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 728) hydrogen bonds : angle 4.24931 ( 2172) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.41404 ( 8) covalent geometry : bond 0.00353 (12906) covalent geometry : angle 0.56869 (17592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.8816 (tt0) cc_final: 0.8495 (tt0) REVERT: A 250 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: A 353 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.7886 (p) REVERT: A 354 MET cc_start: 0.9295 (mmm) cc_final: 0.9069 (mmt) REVERT: A 356 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8730 (mt-10) REVERT: A 551 MET cc_start: 0.8346 (ptm) cc_final: 0.8036 (ptt) REVERT: L 4 MET cc_start: 0.7250 (mmm) cc_final: 0.7041 (tmm) REVERT: H 5 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8128 (mm110) REVERT: H 27 ASP cc_start: 0.7811 (t0) cc_final: 0.7405 (t0) REVERT: H 33 TYR cc_start: 0.8560 (m-80) cc_final: 0.8357 (m-80) REVERT: H 82 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6933 (mp10) REVERT: H 102 TYR cc_start: 0.8963 (m-10) cc_final: 0.8756 (m-10) REVERT: B 225 GLU cc_start: 0.8835 (tt0) cc_final: 0.8502 (mt-10) REVERT: B 249 MET cc_start: 0.9333 (mmm) cc_final: 0.9053 (tpp) REVERT: B 250 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: B 353 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 356 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 359 ASP cc_start: 0.8654 (m-30) cc_final: 0.8433 (m-30) REVERT: B 551 MET cc_start: 0.8413 (ptm) cc_final: 0.8049 (ptt) REVERT: M 4 MET cc_start: 0.7262 (mmm) cc_final: 0.7048 (tmm) REVERT: I 5 GLN cc_start: 0.9012 (tp40) cc_final: 0.8789 (mm110) REVERT: I 20 LEU cc_start: 0.9090 (mp) cc_final: 0.8836 (mt) REVERT: I 27 ASP cc_start: 0.7740 (t0) cc_final: 0.7210 (t0) REVERT: I 33 TYR cc_start: 0.8408 (m-80) cc_final: 0.8158 (m-80) REVERT: I 47 GLU cc_start: 0.8286 (tt0) cc_final: 0.8065 (tt0) REVERT: I 49 MET cc_start: 0.9011 (mmm) cc_final: 0.8802 (mmm) REVERT: I 82 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6914 (mp10) outliers start: 30 outliers final: 18 residues processed: 167 average time/residue: 0.2157 time to fit residues: 54.6331 Evaluate side-chains 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.042727 restraints weight = 62551.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044219 restraints weight = 28863.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.045239 restraints weight = 17316.029| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12910 Z= 0.206 Angle : 0.600 7.440 17600 Z= 0.303 Chirality : 0.039 0.157 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.634 42.219 1752 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.27 % Allowed : 17.19 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1618 helix: 2.72 (0.18), residues: 818 sheet: -0.91 (0.34), residues: 214 loop : -0.64 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 35 HIS 0.004 0.001 HIS B 230 PHE 0.031 0.002 PHE A 213 TYR 0.018 0.002 TYR I 33 ARG 0.009 0.001 ARG M 18 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 728) hydrogen bonds : angle 4.37381 ( 2172) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.35645 ( 8) covalent geometry : bond 0.00471 (12906) covalent geometry : angle 0.60038 (17592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.8810 (tt0) cc_final: 0.8271 (tt0) REVERT: A 250 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: A 253 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 353 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 354 MET cc_start: 0.9289 (mmm) cc_final: 0.9064 (mmt) REVERT: A 356 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8591 (mt-10) REVERT: A 551 MET cc_start: 0.8358 (ptm) cc_final: 0.8051 (ptt) REVERT: A 576 MET cc_start: 0.7031 (tpt) cc_final: 0.6706 (tpp) REVERT: L 4 MET cc_start: 0.7450 (mmm) cc_final: 0.7240 (tmm) REVERT: H 5 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: H 27 ASP cc_start: 0.7813 (t0) cc_final: 0.7387 (t0) REVERT: H 82 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6923 (mp10) REVERT: B 225 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: B 250 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: B 353 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8540 (p) REVERT: B 356 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 359 ASP cc_start: 0.8646 (m-30) cc_final: 0.8434 (m-30) REVERT: B 551 MET cc_start: 0.8326 (ptm) cc_final: 0.8033 (ptt) REVERT: M 4 MET cc_start: 0.7469 (mmm) cc_final: 0.7249 (tmm) REVERT: I 5 GLN cc_start: 0.9012 (tp40) cc_final: 0.8724 (mm110) REVERT: I 27 ASP cc_start: 0.7710 (t0) cc_final: 0.7156 (t0) REVERT: I 33 TYR cc_start: 0.8512 (m-80) cc_final: 0.8187 (m-80) REVERT: I 47 GLU cc_start: 0.8315 (tt0) cc_final: 0.8077 (tt0) REVERT: I 49 MET cc_start: 0.8995 (mmm) cc_final: 0.8785 (mmm) REVERT: I 82 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7042 (mp10) outliers start: 44 outliers final: 24 residues processed: 168 average time/residue: 0.2157 time to fit residues: 55.3810 Evaluate side-chains 154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 62 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.043558 restraints weight = 61676.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.045042 restraints weight = 28381.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.046113 restraints weight = 16696.629| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12910 Z= 0.172 Angle : 0.598 7.309 17600 Z= 0.299 Chirality : 0.040 0.206 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.585 40.900 1752 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.27 % Allowed : 17.56 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1618 helix: 2.68 (0.18), residues: 816 sheet: -0.81 (0.33), residues: 214 loop : -0.61 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.003 0.001 HIS B 230 PHE 0.022 0.002 PHE A 213 TYR 0.027 0.002 TYR H 33 ARG 0.003 0.000 ARG M 18 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 728) hydrogen bonds : angle 4.32086 ( 2172) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.39235 ( 8) covalent geometry : bond 0.00398 (12906) covalent geometry : angle 0.59776 (17592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.8799 (tt0) cc_final: 0.8241 (tt0) REVERT: A 250 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: A 253 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9082 (tp) REVERT: A 353 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.7858 (p) REVERT: A 354 MET cc_start: 0.9298 (mmm) cc_final: 0.9074 (mmt) REVERT: A 356 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 551 MET cc_start: 0.8318 (ptm) cc_final: 0.8021 (ptt) REVERT: A 576 MET cc_start: 0.6874 (tpt) cc_final: 0.6530 (tpt) REVERT: H 27 ASP cc_start: 0.7952 (t0) cc_final: 0.7477 (t0) REVERT: H 33 TYR cc_start: 0.8419 (m-80) cc_final: 0.8140 (m-80) REVERT: B 225 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: B 250 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: B 353 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 356 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 359 ASP cc_start: 0.8684 (m-30) cc_final: 0.8479 (m-30) REVERT: B 412 MET cc_start: 0.8796 (mtp) cc_final: 0.8534 (mtt) REVERT: B 551 MET cc_start: 0.8300 (ptm) cc_final: 0.8004 (ptt) REVERT: I 5 GLN cc_start: 0.8997 (tp40) cc_final: 0.8650 (tm-30) REVERT: I 20 LEU cc_start: 0.9145 (mp) cc_final: 0.8921 (mt) REVERT: I 27 ASP cc_start: 0.7902 (t0) cc_final: 0.7460 (t0) REVERT: I 33 TYR cc_start: 0.8522 (m-80) cc_final: 0.8191 (m-80) outliers start: 44 outliers final: 29 residues processed: 170 average time/residue: 0.2520 time to fit residues: 65.8356 Evaluate side-chains 160 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.044129 restraints weight = 61528.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.045627 restraints weight = 28034.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046710 restraints weight = 16305.007| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12910 Z= 0.135 Angle : 0.591 8.121 17600 Z= 0.292 Chirality : 0.039 0.168 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.504 40.232 1752 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.20 % Allowed : 18.08 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1618 helix: 2.63 (0.18), residues: 826 sheet: -0.55 (0.34), residues: 214 loop : -0.67 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.003 0.001 HIS A 171 PHE 0.019 0.001 PHE A 213 TYR 0.020 0.001 TYR H 33 ARG 0.005 0.000 ARG M 18 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 728) hydrogen bonds : angle 4.23310 ( 2172) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.76907 ( 8) covalent geometry : bond 0.00321 (12906) covalent geometry : angle 0.59089 (17592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.8763 (tt0) cc_final: 0.8262 (tt0) REVERT: A 250 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: A 253 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 328 SER cc_start: 0.9503 (OUTLIER) cc_final: 0.9255 (p) REVERT: A 353 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 356 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8570 (mt-10) REVERT: A 551 MET cc_start: 0.8270 (ptm) cc_final: 0.8005 (ptt) REVERT: A 576 MET cc_start: 0.6896 (tpt) cc_final: 0.6543 (tpt) REVERT: L 17 ASP cc_start: 0.7639 (m-30) cc_final: 0.7380 (m-30) REVERT: L 24 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7904 (mmmt) REVERT: H 5 GLN cc_start: 0.9063 (tp40) cc_final: 0.8668 (tm-30) REVERT: H 27 ASP cc_start: 0.7933 (t0) cc_final: 0.7464 (t0) REVERT: H 33 TYR cc_start: 0.8408 (m-80) cc_final: 0.8129 (m-80) REVERT: H 82 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6783 (mp10) REVERT: B 225 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: B 250 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 353 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8138 (p) REVERT: B 356 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 359 ASP cc_start: 0.8679 (m-30) cc_final: 0.8475 (m-30) REVERT: B 412 MET cc_start: 0.8755 (mtp) cc_final: 0.8462 (mtt) REVERT: B 551 MET cc_start: 0.8259 (ptm) cc_final: 0.7999 (ptt) REVERT: B 576 MET cc_start: 0.6783 (tpt) cc_final: 0.6525 (tpp) REVERT: M 17 ASP cc_start: 0.7634 (m-30) cc_final: 0.7379 (m-30) REVERT: I 5 GLN cc_start: 0.9003 (tp40) cc_final: 0.8659 (tm-30) REVERT: I 27 ASP cc_start: 0.7937 (t0) cc_final: 0.7578 (t0) REVERT: I 33 TYR cc_start: 0.8467 (m-80) cc_final: 0.8151 (m-80) REVERT: I 49 MET cc_start: 0.8866 (mmm) cc_final: 0.8526 (mpp) REVERT: I 82 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6798 (mp10) outliers start: 43 outliers final: 30 residues processed: 174 average time/residue: 0.2888 time to fit residues: 74.1276 Evaluate side-chains 163 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN B 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.045664 restraints weight = 60214.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.047190 restraints weight = 27603.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048273 restraints weight = 16350.557| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12910 Z= 0.112 Angle : 0.601 8.552 17600 Z= 0.292 Chirality : 0.039 0.176 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.309 38.935 1752 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.53 % Allowed : 18.90 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1618 helix: 2.70 (0.18), residues: 826 sheet: -0.12 (0.35), residues: 210 loop : -0.67 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 35 HIS 0.003 0.001 HIS A 171 PHE 0.016 0.001 PHE A 213 TYR 0.015 0.001 TYR H 33 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 728) hydrogen bonds : angle 4.10932 ( 2172) SS BOND : bond 0.00325 ( 4) SS BOND : angle 0.68261 ( 8) covalent geometry : bond 0.00263 (12906) covalent geometry : angle 0.60140 (17592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 328 SER cc_start: 0.9477 (OUTLIER) cc_final: 0.9233 (p) REVERT: A 412 MET cc_start: 0.8763 (mtp) cc_final: 0.8447 (mtt) REVERT: A 551 MET cc_start: 0.8195 (ptm) cc_final: 0.7904 (ptt) REVERT: A 576 MET cc_start: 0.6688 (tpt) cc_final: 0.6331 (tpt) REVERT: L 103 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8615 (tptp) REVERT: H 5 GLN cc_start: 0.9025 (tp40) cc_final: 0.8669 (tm-30) REVERT: H 27 ASP cc_start: 0.7938 (t0) cc_final: 0.7494 (t0) REVERT: H 47 GLU cc_start: 0.8167 (tt0) cc_final: 0.7756 (pt0) REVERT: H 49 MET cc_start: 0.8827 (mmm) cc_final: 0.8239 (mpp) REVERT: H 82 GLN cc_start: 0.7629 (mm-40) cc_final: 0.6963 (mp10) REVERT: B 225 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: B 328 SER cc_start: 0.9454 (OUTLIER) cc_final: 0.9225 (p) REVERT: B 353 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 356 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8531 (mt-10) REVERT: B 359 ASP cc_start: 0.8685 (m-30) cc_final: 0.8407 (m-30) REVERT: B 412 MET cc_start: 0.8691 (mtp) cc_final: 0.8408 (mtt) REVERT: B 551 MET cc_start: 0.8199 (ptm) cc_final: 0.7909 (ptt) REVERT: B 576 MET cc_start: 0.6591 (tpt) cc_final: 0.6315 (tpt) REVERT: M 69 THR cc_start: 0.8679 (p) cc_final: 0.8319 (t) REVERT: M 103 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8617 (tptp) REVERT: I 5 GLN cc_start: 0.8993 (tp40) cc_final: 0.8662 (tm-30) REVERT: I 27 ASP cc_start: 0.8085 (t0) cc_final: 0.7756 (t0) REVERT: I 49 MET cc_start: 0.8842 (mmm) cc_final: 0.8468 (mpp) REVERT: I 82 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6823 (mp10) outliers start: 34 outliers final: 21 residues processed: 170 average time/residue: 0.2139 time to fit residues: 55.9669 Evaluate side-chains 157 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.044912 restraints weight = 60478.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.046452 restraints weight = 27771.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047365 restraints weight = 16390.981| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12910 Z= 0.122 Angle : 0.597 9.725 17600 Z= 0.290 Chirality : 0.039 0.164 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.335 40.409 1752 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 19.49 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1618 helix: 2.68 (0.18), residues: 824 sheet: -0.19 (0.35), residues: 214 loop : -0.63 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35 HIS 0.004 0.001 HIS A 171 PHE 0.027 0.001 PHE A 213 TYR 0.021 0.001 TYR I 33 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 728) hydrogen bonds : angle 4.12426 ( 2172) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.60061 ( 8) covalent geometry : bond 0.00290 (12906) covalent geometry : angle 0.59713 (17592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.9217 (p) REVERT: A 551 MET cc_start: 0.8248 (ptm) cc_final: 0.7943 (ptt) REVERT: A 576 MET cc_start: 0.6728 (tpt) cc_final: 0.6361 (tpt) REVERT: H 5 GLN cc_start: 0.8994 (tp40) cc_final: 0.8644 (tm-30) REVERT: H 27 ASP cc_start: 0.8131 (t0) cc_final: 0.7769 (t0) REVERT: H 49 MET cc_start: 0.8849 (mmm) cc_final: 0.8280 (mpp) REVERT: H 82 GLN cc_start: 0.7618 (mm-40) cc_final: 0.6959 (mp10) REVERT: B 225 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: B 328 SER cc_start: 0.9478 (OUTLIER) cc_final: 0.9239 (p) REVERT: B 359 ASP cc_start: 0.8747 (m-30) cc_final: 0.8497 (m-30) REVERT: B 551 MET cc_start: 0.8249 (ptm) cc_final: 0.7958 (ptt) REVERT: B 576 MET cc_start: 0.6643 (tpt) cc_final: 0.6350 (tpt) REVERT: I 5 GLN cc_start: 0.8988 (tp40) cc_final: 0.8660 (tm-30) REVERT: I 27 ASP cc_start: 0.8132 (t0) cc_final: 0.7783 (t0) REVERT: I 49 MET cc_start: 0.8874 (mmm) cc_final: 0.8503 (mpp) REVERT: I 82 GLN cc_start: 0.7649 (mm-40) cc_final: 0.6991 (mp10) outliers start: 25 outliers final: 20 residues processed: 151 average time/residue: 0.2014 time to fit residues: 48.5584 Evaluate side-chains 150 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 124 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.044771 restraints weight = 60849.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.046303 restraints weight = 28029.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047206 restraints weight = 16718.656| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12910 Z= 0.126 Angle : 0.595 8.861 17600 Z= 0.291 Chirality : 0.039 0.165 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.347 40.301 1752 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.79 % Allowed : 20.01 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1618 helix: 2.67 (0.18), residues: 826 sheet: -0.15 (0.35), residues: 214 loop : -0.62 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35 HIS 0.003 0.001 HIS A 171 PHE 0.027 0.001 PHE A 213 TYR 0.022 0.001 TYR I 33 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 728) hydrogen bonds : angle 4.10401 ( 2172) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.51629 ( 8) covalent geometry : bond 0.00300 (12906) covalent geometry : angle 0.59533 (17592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.37 seconds wall clock time: 68 minutes 36.75 seconds (4116.75 seconds total)