Starting phenix.real_space_refine on Thu Sep 18 00:42:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tqq_8435/09_2025/5tqq_8435.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tqq_8435/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5tqq_8435/09_2025/5tqq_8435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tqq_8435/09_2025/5tqq_8435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tqq_8435/09_2025/5tqq_8435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tqq_8435/09_2025/5tqq_8435.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 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: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 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: 3.54, per 1000 atoms: 0.28 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: 1.13 Conformation dependent library (CDL) restraints added in 606.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.51 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: 2.33 Time building geometry restraints manager: 1.49 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: 0.02 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.980 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- 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 : 6.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (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 ARG 0.007 0.001 ARG H 98 TYR 0.022 0.002 TYR B 138 PHE 0.027 0.003 PHE A 410 TRP 0.015 0.002 TRP B 411 HIS 0.009 0.002 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00821 (12906) covalent geometry : angle 1.51705 (17592) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.29547 ( 8) hydrogen bonds : bond 0.15807 ( 728) hydrogen bonds : angle 6.13555 ( 2172) *********************** 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 : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7951 (t80) REVERT: A 353 SER cc_start: 0.8571 (t) cc_final: 0.8330 (p) REVERT: A 356 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8786 (mt-10) 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: 0.8517 (mtt) REVERT: A 482 ILE cc_start: 0.8970 (pt) cc_final: 0.8695 (pt) 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: 0.7594 (t80) REVERT: L 61 ARG cc_start: 0.7784 (ptt90) cc_final: 0.7160 (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: 0.8058 (m-30) REVERT: H 33 TYR cc_start: 0.7983 (m-80) cc_final: 0.7763 (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: 0.8327 (mmm) REVERT: H 67 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8168 (mtm180) REVERT: H 82 GLN cc_start: 0.8919 (mt0) cc_final: 0.8557 (mp10) REVERT: H 101 ASP cc_start: 0.9081 (m-30) cc_final: 0.8849 (m-30) REVERT: B 140 ASP cc_start: 0.8069 (t0) cc_final: 0.7653 (t70) REVERT: B 217 PHE cc_start: 0.8193 (m-80) cc_final: 0.7856 (m-80) REVERT: B 231 PHE cc_start: 0.8403 (m-80) cc_final: 0.8087 (m-80) REVERT: B 240 PHE cc_start: 0.8313 (t80) cc_final: 0.7810 (t80) REVERT: B 359 ASP cc_start: 0.8834 (m-30) cc_final: 0.8606 (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: 0.8521 (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: 0.7498 (t80) REVERT: M 61 ARG cc_start: 0.7754 (ptt90) cc_final: 0.7134 (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: 0.8075 (m-30) REVERT: I 33 TYR cc_start: 0.8000 (m-80) cc_final: 0.7781 (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: 0.8325 (mmm) REVERT: I 67 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8173 (mtm180) REVERT: I 82 GLN cc_start: 0.8915 (mt0) cc_final: 0.8552 (mp10) REVERT: I 101 ASP cc_start: 0.9068 (m-30) cc_final: 0.8829 (m-30) outliers start: 12 outliers final: 2 residues processed: 320 average time/residue: 0.1219 time to fit residues: 56.0950 Evaluate side-chains 183 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.2998 r_free = 0.2998 target = 0.054004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.045264 restraints weight = 61236.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.046838 restraints weight = 27822.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.047866 restraints weight = 16392.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.048605 restraints weight = 11352.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.049146 restraints weight = 8621.001| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2604 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 : 0.646 12.344 17600 Z= 0.322 Chirality : 0.042 0.164 2032 Planarity : 0.005 0.051 2188 Dihedral : 4.970 54.651 1752 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.86 % Allowed : 13.62 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.22), residues: 1618 helix: 3.58 (0.18), residues: 808 sheet: -1.50 (0.33), residues: 210 loop : -1.54 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.013 0.002 TYR A 236 PHE 0.020 0.002 PHE B 52 TRP 0.009 0.001 TRP I 103 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00314 (12906) covalent geometry : angle 0.64564 (17592) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.55864 ( 8) hydrogen bonds : bond 0.04055 ( 728) hydrogen bonds : angle 4.57526 ( 2172) *********************** 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 220 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.9213 (mtp) cc_final: 0.8974 (mtp) REVERT: A 240 PHE cc_start: 0.8575 (t80) cc_final: 0.8197 (t80) REVERT: A 412 MET cc_start: 0.8742 (mtp) cc_final: 0.8505 (mtt) REVERT: A 551 MET cc_start: 0.8471 (ptm) cc_final: 0.8103 (ptt) REVERT: L 4 MET cc_start: 0.7853 (mmm) cc_final: 0.7216 (mmm) REVERT: L 24 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8240 (mmmt) REVERT: L 61 ARG cc_start: 0.7863 (ptt90) cc_final: 0.7304 (ptt90) REVERT: H 32 ASP cc_start: 0.8387 (t0) cc_final: 0.7763 (m-30) REVERT: H 49 MET cc_start: 0.9098 (mmm) cc_final: 0.8768 (mmm) REVERT: B 175 MET cc_start: 0.9219 (mtp) cc_final: 0.8970 (mtp) REVERT: B 240 PHE cc_start: 0.8639 (t80) cc_final: 0.8198 (t80) REVERT: B 356 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8642 (mt-10) REVERT: B 359 ASP cc_start: 0.8395 (m-30) cc_final: 0.7977 (m-30) REVERT: B 412 MET cc_start: 0.8741 (mtp) cc_final: 0.8516 (mtt) REVERT: B 503 MET cc_start: 0.8905 (ttm) cc_final: 0.8364 (mtm) REVERT: B 551 MET cc_start: 0.8451 (ptm) cc_final: 0.8102 (ptt) REVERT: M 4 MET cc_start: 0.7849 (mmm) cc_final: 0.7293 (mmm) REVERT: M 6 GLN cc_start: 0.8206 (pm20) cc_final: 0.7985 (pm20) REVERT: M 61 ARG cc_start: 0.7873 (ptt90) cc_final: 0.7331 (ptt90) REVERT: I 32 ASP cc_start: 0.8403 (t0) cc_final: 0.7782 (m-30) REVERT: I 49 MET cc_start: 0.9070 (mmm) cc_final: 0.8728 (mmm) outliers start: 25 outliers final: 10 residues processed: 216 average time/residue: 0.1277 time to fit residues: 39.2236 Evaluate side-chains 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET 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 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 69 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 160 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 0.0060 chunk 97 optimal weight: 0.0010 chunk 95 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- 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 I 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.045649 restraints weight = 61393.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.047182 restraints weight = 27685.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.048240 restraints weight = 16366.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.048986 restraints weight = 11167.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.049445 restraints weight = 8394.614| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12910 Z= 0.118 Angle : 0.585 9.274 17600 Z= 0.293 Chirality : 0.039 0.147 2032 Planarity : 0.005 0.045 2188 Dihedral : 4.505 44.193 1752 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.22), residues: 1618 helix: 3.34 (0.18), residues: 812 sheet: -1.26 (0.33), residues: 212 loop : -1.31 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.012 0.001 TYR B 236 PHE 0.016 0.001 PHE A 52 TRP 0.009 0.001 TRP I 48 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00266 (12906) covalent geometry : angle 0.58468 (17592) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.41508 ( 8) hydrogen bonds : bond 0.03388 ( 728) hydrogen bonds : angle 4.17129 ( 2172) *********************** 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: 23 poor density : 175 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8706 (t0) cc_final: 0.8478 (t70) REVERT: A 175 MET cc_start: 0.9135 (mtp) cc_final: 0.8892 (mtp) REVERT: A 225 GLU cc_start: 0.8770 (tt0) cc_final: 0.8395 (mt-10) REVERT: A 240 PHE cc_start: 0.8559 (t80) cc_final: 0.7997 (t80) REVERT: A 359 ASP cc_start: 0.8604 (t0) cc_final: 0.8370 (m-30) REVERT: A 408 MET cc_start: 0.9010 (mmp) cc_final: 0.8726 (mmp) REVERT: A 427 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8981 (mmt) REVERT: A 503 MET cc_start: 0.8870 (ttm) cc_final: 0.8144 (mtp) REVERT: A 551 MET cc_start: 0.8354 (ptm) cc_final: 0.8033 (ptt) REVERT: H 27 ASP cc_start: 0.7599 (t0) cc_final: 0.7324 (t0) REVERT: H 32 ASP cc_start: 0.8372 (t0) cc_final: 0.7803 (m-30) REVERT: H 47 GLU cc_start: 0.8043 (tt0) cc_final: 0.7683 (pt0) REVERT: B 175 MET cc_start: 0.9123 (mtp) cc_final: 0.8877 (mtp) REVERT: B 225 GLU cc_start: 0.8819 (tt0) cc_final: 0.8483 (mt-10) REVERT: B 231 PHE cc_start: 0.7576 (m-80) cc_final: 0.7327 (m-80) REVERT: B 240 PHE cc_start: 0.8551 (t80) cc_final: 0.7948 (t80) REVERT: B 359 ASP cc_start: 0.8347 (m-30) cc_final: 0.7910 (m-30) REVERT: B 408 MET cc_start: 0.9006 (mmp) cc_final: 0.8732 (mmp) REVERT: B 427 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8926 (mmt) REVERT: B 503 MET cc_start: 0.8852 (ttm) cc_final: 0.8645 (mtp) REVERT: B 551 MET cc_start: 0.8431 (ptm) cc_final: 0.8066 (ptt) REVERT: M 4 MET cc_start: 0.7827 (mmm) cc_final: 0.7156 (tmm) REVERT: M 10 PHE cc_start: 0.9058 (m-80) cc_final: 0.8773 (m-80) REVERT: M 103 LYS cc_start: 0.9259 (ttmm) cc_final: 0.8977 (mtpp) REVERT: I 27 ASP cc_start: 0.7391 (t0) cc_final: 0.6921 (t0) REVERT: I 32 ASP cc_start: 0.8387 (t0) cc_final: 0.7827 (m-30) REVERT: I 47 GLU cc_start: 0.8061 (tt0) cc_final: 0.7686 (pt0) REVERT: I 101 ASP cc_start: 0.8596 (p0) cc_final: 0.8394 (p0) outliers start: 23 outliers final: 12 residues processed: 189 average time/residue: 0.1148 time to fit residues: 32.1652 Evaluate side-chains 158 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 96 LEU 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 358 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 24 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 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 652 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 652 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.041765 restraints weight = 63630.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.043198 restraints weight = 29237.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.044161 restraints weight = 17491.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.044810 restraints weight = 12186.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.045289 restraints weight = 9336.239| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12910 Z= 0.287 Angle : 0.685 7.653 17600 Z= 0.351 Chirality : 0.042 0.151 2032 Planarity : 0.005 0.039 2188 Dihedral : 5.035 50.201 1752 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.32 % Allowed : 16.22 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1618 helix: 2.50 (0.18), residues: 826 sheet: -1.34 (0.33), residues: 212 loop : -0.96 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 536 TYR 0.025 0.003 TYR I 33 PHE 0.023 0.002 PHE I 79 TRP 0.016 0.002 TRP B 391 HIS 0.007 0.002 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00639 (12906) covalent geometry : angle 0.68522 (17592) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.27709 ( 8) hydrogen bonds : bond 0.04180 ( 728) hydrogen bonds : angle 4.68947 ( 2172) *********************** 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 198 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8789 (t0) cc_final: 0.8502 (t0) REVERT: A 175 MET cc_start: 0.9225 (mtp) cc_final: 0.8910 (mtp) REVERT: A 250 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: A 551 MET cc_start: 0.8309 (ptm) cc_final: 0.8000 (ptt) REVERT: L 4 MET cc_start: 0.7456 (mmm) cc_final: 0.7127 (mmm) REVERT: L 10 PHE cc_start: 0.8894 (m-10) cc_final: 0.8674 (m-80) REVERT: L 28 ASN cc_start: 0.8772 (t0) cc_final: 0.8494 (t0) REVERT: H 27 ASP cc_start: 0.7837 (t0) cc_final: 0.7391 (t0) REVERT: H 33 TYR cc_start: 0.8583 (m-80) cc_final: 0.8246 (m-80) REVERT: H 102 TYR cc_start: 0.8821 (m-10) cc_final: 0.8486 (m-10) REVERT: B 175 MET cc_start: 0.9270 (mtp) cc_final: 0.8961 (mtp) REVERT: B 225 GLU cc_start: 0.8839 (tt0) cc_final: 0.8341 (mt-10) REVERT: B 231 PHE cc_start: 0.7813 (m-80) cc_final: 0.7609 (m-80) REVERT: B 250 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: B 359 ASP cc_start: 0.8592 (m-30) cc_final: 0.8211 (m-30) REVERT: B 551 MET cc_start: 0.8278 (ptm) cc_final: 0.7981 (ptt) REVERT: M 4 MET cc_start: 0.7528 (mmm) cc_final: 0.6987 (mmm) REVERT: M 28 ASN cc_start: 0.8791 (t0) cc_final: 0.8504 (t0) REVERT: I 5 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: I 27 ASP cc_start: 0.7594 (t0) cc_final: 0.6960 (t0) REVERT: I 33 TYR cc_start: 0.8599 (m-80) cc_final: 0.8252 (m-80) outliers start: 58 outliers final: 27 residues processed: 182 average time/residue: 0.1075 time to fit residues: 29.6213 Evaluate side-chains 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL 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 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE 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 15 VAL 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 5 GLN 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 3 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.043956 restraints weight = 61992.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.045469 restraints weight = 28005.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.046505 restraints weight = 16568.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.047184 restraints weight = 11310.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.047569 restraints weight = 8660.589| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4242 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= 0.131 Angle : 0.578 7.803 17600 Z= 0.290 Chirality : 0.040 0.155 2032 Planarity : 0.004 0.051 2188 Dihedral : 4.553 45.958 1752 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.08 % Allowed : 18.97 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.22), residues: 1618 helix: 2.69 (0.18), residues: 816 sheet: -1.21 (0.33), residues: 212 loop : -0.80 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 18 TYR 0.015 0.001 TYR B 236 PHE 0.023 0.002 PHE A 213 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00307 (12906) covalent geometry : angle 0.57849 (17592) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.43222 ( 8) hydrogen bonds : bond 0.03357 ( 728) hydrogen bonds : angle 4.21739 ( 2172) *********************** 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 171 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.9181 (mtp) cc_final: 0.8899 (mtp) REVERT: A 250 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: A 551 MET cc_start: 0.8303 (ptm) cc_final: 0.8010 (ptt) REVERT: L 28 ASN cc_start: 0.8870 (t0) cc_final: 0.8517 (t0) REVERT: H 27 ASP cc_start: 0.7806 (t0) cc_final: 0.7343 (t0) REVERT: H 33 TYR cc_start: 0.8450 (m-80) cc_final: 0.8186 (m-80) REVERT: B 225 GLU cc_start: 0.8857 (tt0) cc_final: 0.8456 (mt-10) REVERT: B 250 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: B 359 ASP cc_start: 0.8582 (m-30) cc_final: 0.8247 (m-30) REVERT: B 551 MET cc_start: 0.8306 (ptm) cc_final: 0.8013 (ptt) REVERT: M 4 MET cc_start: 0.7542 (mmm) cc_final: 0.7205 (mmm) REVERT: M 28 ASN cc_start: 0.8878 (t0) cc_final: 0.8531 (t0) REVERT: I 5 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: I 27 ASP cc_start: 0.7827 (t0) cc_final: 0.7385 (t0) REVERT: I 33 TYR cc_start: 0.8491 (m-80) cc_final: 0.8215 (m-80) REVERT: I 102 TYR cc_start: 0.8910 (m-10) cc_final: 0.8649 (m-10) outliers start: 28 outliers final: 16 residues processed: 164 average time/residue: 0.1051 time to fit residues: 26.2273 Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 525 ILE 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 B residue 250 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 47 LEU 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 5 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 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 = 0.2959 r_free = 0.2959 target = 0.052578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.044170 restraints weight = 61738.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.045683 restraints weight = 28166.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.046732 restraints weight = 16747.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047454 restraints weight = 11461.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047922 restraints weight = 8672.129| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12910 Z= 0.127 Angle : 0.576 7.737 17600 Z= 0.289 Chirality : 0.039 0.161 2032 Planarity : 0.004 0.041 2188 Dihedral : 4.403 41.699 1752 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.12 % Allowed : 17.93 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.22), residues: 1618 helix: 2.58 (0.18), residues: 826 sheet: -0.99 (0.34), residues: 212 loop : -0.81 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 18 TYR 0.014 0.001 TYR A 236 PHE 0.026 0.001 PHE B 213 TRP 0.008 0.001 TRP A 234 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00301 (12906) covalent geometry : angle 0.57628 (17592) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.53354 ( 8) hydrogen bonds : bond 0.03305 ( 728) hydrogen bonds : angle 4.17327 ( 2172) *********************** 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 186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8781 (p0) cc_final: 0.8571 (p0) REVERT: A 253 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9054 (tp) REVERT: A 551 MET cc_start: 0.8277 (ptm) cc_final: 0.7985 (ptt) REVERT: L 4 MET cc_start: 0.7157 (mmm) cc_final: 0.6614 (tpt) REVERT: L 28 ASN cc_start: 0.8905 (t0) cc_final: 0.8568 (t0) REVERT: H 5 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7927 (mm110) REVERT: H 27 ASP cc_start: 0.7795 (t0) cc_final: 0.7327 (t0) REVERT: H 82 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6829 (mp10) REVERT: B 225 GLU cc_start: 0.8698 (tt0) cc_final: 0.8476 (tt0) REVERT: B 231 PHE cc_start: 0.7618 (m-80) cc_final: 0.7336 (m-80) REVERT: B 359 ASP cc_start: 0.8618 (m-30) cc_final: 0.8275 (m-30) REVERT: B 551 MET cc_start: 0.8269 (ptm) cc_final: 0.7979 (ptt) REVERT: M 4 MET cc_start: 0.7521 (mmm) cc_final: 0.7232 (mmm) REVERT: M 28 ASN cc_start: 0.8916 (t0) cc_final: 0.8569 (t0) REVERT: I 5 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7929 (mm110) REVERT: I 27 ASP cc_start: 0.7819 (t0) cc_final: 0.7361 (t0) REVERT: I 82 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6803 (mp10) outliers start: 42 outliers final: 24 residues processed: 172 average time/residue: 0.1032 time to fit residues: 27.1879 Evaluate side-chains 157 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU 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 L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LEU 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 B residue 235 ASP 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 652 ASN 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 5 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 129 optimal weight: 0.0370 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 161 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 B 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.053295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.044945 restraints weight = 61240.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.046471 restraints weight = 28055.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047518 restraints weight = 16701.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048261 restraints weight = 11441.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.048749 restraints weight = 8619.063| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12910 Z= 0.116 Angle : 0.577 7.967 17600 Z= 0.288 Chirality : 0.040 0.201 2032 Planarity : 0.004 0.041 2188 Dihedral : 4.244 35.658 1752 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.68 % Allowed : 18.38 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.22), residues: 1618 helix: 2.58 (0.18), residues: 828 sheet: -0.69 (0.35), residues: 212 loop : -0.72 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 595 TYR 0.021 0.001 TYR H 33 PHE 0.017 0.001 PHE H 79 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00272 (12906) covalent geometry : angle 0.57742 (17592) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.58728 ( 8) hydrogen bonds : bond 0.03137 ( 728) hydrogen bonds : angle 4.09276 ( 2172) *********************** 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 183 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8779 (p0) cc_final: 0.8573 (p0) REVERT: A 253 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9042 (tp) REVERT: A 551 MET cc_start: 0.8179 (ptm) cc_final: 0.7915 (ptt) REVERT: H 5 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7901 (mm110) REVERT: H 27 ASP cc_start: 0.7833 (t0) cc_final: 0.7333 (t0) REVERT: H 47 GLU cc_start: 0.8029 (tt0) cc_final: 0.7583 (pt0) REVERT: H 49 MET cc_start: 0.8877 (mmm) cc_final: 0.8197 (mpp) REVERT: H 82 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6712 (mp10) REVERT: B 231 PHE cc_start: 0.7590 (m-80) cc_final: 0.7364 (m-80) REVERT: B 253 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9047 (tp) REVERT: B 359 ASP cc_start: 0.8437 (m-30) cc_final: 0.8102 (t0) REVERT: B 551 MET cc_start: 0.8197 (ptm) cc_final: 0.7951 (ptt) REVERT: M 4 MET cc_start: 0.7487 (mmm) cc_final: 0.7222 (mmm) REVERT: M 24 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7784 (mmmt) REVERT: M 28 ASN cc_start: 0.8958 (t0) cc_final: 0.8751 (t0) REVERT: I 5 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7904 (mm110) REVERT: I 27 ASP cc_start: 0.7867 (t0) cc_final: 0.7374 (t0) REVERT: I 47 GLU cc_start: 0.8150 (tt0) cc_final: 0.7763 (pt0) REVERT: I 49 MET cc_start: 0.8875 (mmm) cc_final: 0.8207 (mpp) REVERT: I 82 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6589 (mp10) outliers start: 36 outliers final: 27 residues processed: 170 average time/residue: 0.1087 time to fit residues: 27.8285 Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU 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 652 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LEU 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 B residue 115 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 652 ASN 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 Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.045140 restraints weight = 60660.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.046645 restraints weight = 27879.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.047632 restraints weight = 16667.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048415 restraints weight = 11655.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.048631 restraints weight = 8727.839| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4631 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= 0.115 Angle : 0.584 7.876 17600 Z= 0.286 Chirality : 0.039 0.165 2032 Planarity : 0.004 0.041 2188 Dihedral : 4.103 28.949 1752 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.05 % Allowed : 17.86 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.22), residues: 1618 helix: 2.62 (0.18), residues: 828 sheet: -0.52 (0.35), residues: 212 loop : -0.72 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 18 TYR 0.020 0.001 TYR H 33 PHE 0.017 0.001 PHE I 79 TRP 0.008 0.001 TRP A 234 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00274 (12906) covalent geometry : angle 0.58388 (17592) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.45020 ( 8) hydrogen bonds : bond 0.03076 ( 728) hydrogen bonds : angle 4.05827 ( 2172) *********************** 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 182 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.508 Fit side-chains REVERT: A 137 ASP cc_start: 0.8799 (p0) cc_final: 0.8572 (p0) REVERT: A 250 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: A 253 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9070 (tp) REVERT: A 551 MET cc_start: 0.8179 (ptm) cc_final: 0.7922 (ptt) REVERT: A 576 MET cc_start: 0.6965 (tpt) cc_final: 0.6654 (tpp) REVERT: L 24 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8008 (mmmt) REVERT: L 103 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8633 (tptp) REVERT: H 5 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8006 (mm110) REVERT: H 27 ASP cc_start: 0.7931 (t0) cc_final: 0.7438 (t0) REVERT: H 47 GLU cc_start: 0.8142 (tt0) cc_final: 0.7725 (pt0) REVERT: H 49 MET cc_start: 0.8880 (mmm) cc_final: 0.8209 (mpp) REVERT: H 82 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6950 (mp10) REVERT: B 250 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: B 253 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9073 (tp) REVERT: B 359 ASP cc_start: 0.8391 (m-30) cc_final: 0.8099 (t0) REVERT: B 551 MET cc_start: 0.8185 (ptm) cc_final: 0.7919 (ptt) REVERT: M 4 MET cc_start: 0.7500 (mmm) cc_final: 0.7275 (mmm) REVERT: M 24 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7877 (mmmt) REVERT: M 28 ASN cc_start: 0.8957 (t0) cc_final: 0.8729 (t0) REVERT: M 103 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8803 (tptp) REVERT: I 5 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7912 (mm110) REVERT: I 27 ASP cc_start: 0.7813 (t0) cc_final: 0.7308 (t0) REVERT: I 47 GLU cc_start: 0.8156 (tt0) cc_final: 0.7732 (pt0) REVERT: I 49 MET cc_start: 0.8875 (mmm) cc_final: 0.8217 (mpp) REVERT: I 82 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6820 (mp10) outliers start: 41 outliers final: 27 residues processed: 169 average time/residue: 0.1029 time to fit residues: 26.5935 Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 LEU 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 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU 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 115 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 320 MET 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 656 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU 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 Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 0.0470 chunk 100 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.044466 restraints weight = 61945.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.045977 restraints weight = 28429.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.046902 restraints weight = 17054.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.047704 restraints weight = 12118.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.048136 restraints weight = 9003.718| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12910 Z= 0.135 Angle : 0.589 7.571 17600 Z= 0.291 Chirality : 0.039 0.167 2032 Planarity : 0.004 0.041 2188 Dihedral : 4.069 21.187 1752 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.90 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1618 helix: 2.63 (0.18), residues: 830 sheet: -0.40 (0.35), residues: 212 loop : -0.68 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.021 0.001 TYR H 33 PHE 0.017 0.001 PHE H 79 TRP 0.014 0.001 TRP I 35 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00322 (12906) covalent geometry : angle 0.58933 (17592) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.66508 ( 8) hydrogen bonds : bond 0.03120 ( 728) hydrogen bonds : angle 4.09204 ( 2172) *********************** 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 172 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8803 (p0) cc_final: 0.8580 (p0) REVERT: A 250 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: A 253 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9086 (tp) REVERT: A 551 MET cc_start: 0.8201 (ptm) cc_final: 0.7938 (ptt) REVERT: A 576 MET cc_start: 0.6918 (tpt) cc_final: 0.6538 (tpt) REVERT: H 5 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7928 (mm110) REVERT: H 27 ASP cc_start: 0.7915 (t0) cc_final: 0.7407 (t0) REVERT: H 47 GLU cc_start: 0.8027 (tt0) cc_final: 0.7561 (pt0) REVERT: H 49 MET cc_start: 0.8883 (mmm) cc_final: 0.8231 (mpp) REVERT: H 82 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7223 (mm-40) REVERT: B 250 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 359 ASP cc_start: 0.8425 (m-30) cc_final: 0.8037 (m-30) REVERT: B 551 MET cc_start: 0.8198 (ptm) cc_final: 0.7934 (ptt) REVERT: B 576 MET cc_start: 0.6976 (tpt) cc_final: 0.6635 (tpt) REVERT: M 24 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8024 (mmmt) REVERT: M 28 ASN cc_start: 0.8976 (t0) cc_final: 0.8776 (t0) REVERT: I 5 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7944 (mm110) REVERT: I 27 ASP cc_start: 0.7877 (t0) cc_final: 0.7384 (t0) REVERT: I 47 GLU cc_start: 0.8045 (tt0) cc_final: 0.7571 (pt0) REVERT: I 49 MET cc_start: 0.8887 (mmm) cc_final: 0.8242 (mpp) REVERT: I 82 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6927 (mp10) outliers start: 39 outliers final: 29 residues processed: 158 average time/residue: 0.0977 time to fit residues: 24.0700 Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 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 358 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU 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 115 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 525 ILE 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 47 LEU 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 Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 145 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.044104 restraints weight = 62045.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.045585 restraints weight = 28626.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046635 restraints weight = 16896.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047350 restraints weight = 11728.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.047798 restraints weight = 8854.973| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12910 Z= 0.152 Angle : 0.602 7.554 17600 Z= 0.296 Chirality : 0.040 0.165 2032 Planarity : 0.004 0.041 2188 Dihedral : 4.136 20.652 1752 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.75 % Allowed : 18.38 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1618 helix: 2.59 (0.18), residues: 830 sheet: -0.32 (0.36), residues: 214 loop : -0.67 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.021 0.001 TYR H 33 PHE 0.017 0.001 PHE H 79 TRP 0.012 0.001 TRP I 35 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00359 (12906) covalent geometry : angle 0.60218 (17592) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.43899 ( 8) hydrogen bonds : bond 0.03196 ( 728) hydrogen bonds : angle 4.14912 ( 2172) ********************** 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 167 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: A 359 ASP cc_start: 0.8608 (t0) cc_final: 0.8382 (m-30) REVERT: A 551 MET cc_start: 0.8208 (ptm) cc_final: 0.7924 (ptt) REVERT: A 576 MET cc_start: 0.6689 (tpt) cc_final: 0.6357 (tpt) REVERT: H 5 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8031 (mm-40) REVERT: H 27 ASP cc_start: 0.7822 (t0) cc_final: 0.7327 (t0) REVERT: H 49 MET cc_start: 0.8881 (mmm) cc_final: 0.8254 (mpp) REVERT: H 82 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7263 (mm-40) REVERT: B 250 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: B 359 ASP cc_start: 0.8428 (m-30) cc_final: 0.8070 (m-30) REVERT: B 551 MET cc_start: 0.8202 (ptm) cc_final: 0.7929 (ptt) REVERT: B 576 MET cc_start: 0.6569 (tpt) cc_final: 0.6308 (tpt) REVERT: M 24 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8341 (mmmt) REVERT: I 5 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: I 27 ASP cc_start: 0.7875 (t0) cc_final: 0.7501 (t0) REVERT: I 49 MET cc_start: 0.8882 (mmm) cc_final: 0.8258 (mpp) REVERT: I 82 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7210 (mm-40) outliers start: 37 outliers final: 28 residues processed: 155 average time/residue: 0.0930 time to fit residues: 22.3371 Evaluate side-chains 156 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE 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 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU 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 115 THR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 47 LEU 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 Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.043670 restraints weight = 62119.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.045153 restraints weight = 28497.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.046233 restraints weight = 16825.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046963 restraints weight = 11543.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047374 restraints weight = 8778.223| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12910 Z= 0.149 Angle : 0.613 10.248 17600 Z= 0.300 Chirality : 0.040 0.167 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.112 19.389 1752 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 18.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1618 helix: 2.56 (0.18), residues: 830 sheet: -0.25 (0.36), residues: 214 loop : -0.64 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.021 0.001 TYR H 33 PHE 0.021 0.001 PHE H 79 TRP 0.013 0.001 TRP I 35 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00354 (12906) covalent geometry : angle 0.61220 (17592) SS BOND : bond 0.00150 ( 4) SS BOND : angle 1.29444 ( 8) hydrogen bonds : bond 0.03215 ( 728) hydrogen bonds : angle 4.16836 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.96 seconds wall clock time: 32 minutes 17.38 seconds (1937.38 seconds total)