Starting phenix.real_space_refine on Tue Jun 10 02:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3u_38899/06_2025/8y3u_38899.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 54 5.16 5 C 7113 2.51 5 N 1927 2.21 5 O 2179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11273 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1195 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1195 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.63, per 1000 atoms: 0.68 Number of scatterers: 11273 At special positions: 0 Unit cell: (82.5, 145.2, 141.9, 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 54 16.00 O 2179 8.00 N 1927 7.00 C 7113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 325 " distance=2.04 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 556 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 260 " - pdb=" SG CYS F 325 " distance=2.04 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 135 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 103 " - pdb=" SG CYS I 108 " distance=2.04 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 325 " distance=2.04 Simple disulfide: pdb=" SG CYS K 511 " - pdb=" SG CYS K 556 " distance=2.03 Simple disulfide: pdb=" SG CYS L 108 " - pdb=" SG CYS L 135 " distance=2.03 Simple disulfide: pdb=" SG CYS L 121 " - pdb=" SG CYS L 147 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2606 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 34 sheets defined 11.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.795A pdb=" N GLY A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'C' and resid 557 through 575 removed outlier: 4.037A pdb=" N LEU C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ALA C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 597 removed outlier: 3.856A pdb=" N ARG C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.657A pdb=" N GLY D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 78 through 84 removed outlier: 4.183A pdb=" N THR D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.744A pdb=" N GLY E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.887A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 575 removed outlier: 5.277A pdb=" N GLN G 567 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 removed outlier: 4.435A pdb=" N ARG G 596 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP G 597 " --> pdb=" O LEU G 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 removed outlier: 3.646A pdb=" N GLY H 74 " --> pdb=" O GLU H 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.111A pdb=" N GLY I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'K' and resid 553 through 575 removed outlier: 5.075A pdb=" N GLN K 567 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA K 568 " --> pdb=" O GLU K 564 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA K 575 " --> pdb=" O LEU K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 597 removed outlier: 3.847A pdb=" N ARG K 596 " --> pdb=" O PHE K 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 74 removed outlier: 3.705A pdb=" N GLY L 74 " --> pdb=" O GLU L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 78 through 84 removed outlier: 4.364A pdb=" N THR L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.012A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 50 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.674A pdb=" N PHE A 113 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 244 removed outlier: 3.505A pdb=" N SER B 244 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 259 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 247 through 249 Processing sheet with id=AA6, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'C' and resid 518 through 519 Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.843A pdb=" N HIS D 39 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 36 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 185 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.843A pdb=" N HIS D 39 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 36 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 185 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 160 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'D' and resid 105 through 114 removed outlier: 6.382A pdb=" N GLU D 106 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS D 139 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS D 108 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 141 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN D 110 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLY D 143 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU D 112 " --> pdb=" O GLY D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.967A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.239A pdb=" N CYS E 96 " --> pdb=" O TRP E 114 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP E 114 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG E 98 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 242 through 244 removed outlier: 4.030A pdb=" N SER F 244 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 259 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE F 308 " --> pdb=" O CYS F 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 247 through 249 removed outlier: 6.795A pdb=" N LEU F 248 " --> pdb=" O GLU F 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 282 through 286 removed outlier: 5.245A pdb=" N TRP F 272 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER F 286 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU F 270 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 514 through 515 Processing sheet with id=AC1, first strand: chain 'G' and resid 518 through 519 Processing sheet with id=AC2, first strand: chain 'G' and resid 580 through 581 removed outlier: 3.670A pdb=" N THR G 581 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 98 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 160 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY H 36 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 35 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 580 through 581 removed outlier: 3.670A pdb=" N THR G 581 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 98 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 160 " --> pdb=" O SER H 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AC5, first strand: chain 'H' and resid 109 through 114 Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.643A pdb=" N MET I 34 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 50 " --> pdb=" O TYR I 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.865A pdb=" N ARG I 98 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 241 through 244 removed outlier: 3.680A pdb=" N SER J 244 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR J 259 " --> pdb=" O SER J 244 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 247 through 249 removed outlier: 3.644A pdb=" N THR J 338 " --> pdb=" O TYR J 323 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU J 270 " --> pdb=" O SER J 286 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER J 286 " --> pdb=" O LEU J 270 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TRP J 272 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 514 through 515 Processing sheet with id=AD3, first strand: chain 'K' and resid 518 through 519 Processing sheet with id=AD4, first strand: chain 'L' and resid 42 through 45 removed outlier: 6.990A pdb=" N GLY L 36 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 42 through 45 removed outlier: 6.990A pdb=" N GLY L 36 " --> pdb=" O ILE L 185 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE L 160 " --> pdb=" O SER L 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 86 through 89 Processing sheet with id=AD7, first strand: chain 'L' and resid 105 through 114 removed outlier: 6.237A pdb=" N GLU L 106 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N HIS L 139 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS L 108 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL L 141 " --> pdb=" O CYS L 108 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN L 110 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY L 143 " --> pdb=" O ASN L 110 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU L 112 " --> pdb=" O GLY L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 357 hydrogen bonds defined for protein. 885 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: 3.70 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3619 1.34 - 1.46: 2946 1.46 - 1.58: 4893 1.58 - 1.70: 1 1.70 - 1.82: 69 Bond restraints: 11528 Sorted by residual: bond pdb=" CB PRO I 41 " pdb=" CG PRO I 41 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.94e+00 bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP D 49 " pdb=" CB ASP D 49 " ideal model delta sigma weight residual 1.524 1.546 -0.021 1.22e-02 6.72e+03 3.06e+00 ... (remaining 11523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 15123 1.73 - 3.47: 395 3.47 - 5.20: 93 5.20 - 6.94: 27 6.94 - 8.67: 2 Bond angle restraints: 15640 Sorted by residual: angle pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" CD PRO I 41 " ideal model delta sigma weight residual 112.00 103.33 8.67 1.40e+00 5.10e-01 3.84e+01 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 113.71 109.48 4.23 9.50e-01 1.11e+00 1.98e+01 angle pdb=" CA ASP H 47 " pdb=" C ASP H 47 " pdb=" N VAL H 48 " ideal model delta sigma weight residual 116.25 120.68 -4.43 1.30e+00 5.92e-01 1.16e+01 angle pdb=" CB LYS E 43 " pdb=" CG LYS E 43 " pdb=" CD LYS E 43 " ideal model delta sigma weight residual 111.30 119.05 -7.75 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA GLN K 595 " pdb=" CB GLN K 595 " pdb=" CG GLN K 595 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 15635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.23: 6311 23.23 - 46.47: 517 46.47 - 69.70: 116 69.70 - 92.93: 28 92.93 - 116.17: 12 Dihedral angle restraints: 6984 sinusoidal: 2874 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS L 108 " pdb=" SG CYS L 108 " pdb=" SG CYS L 135 " pdb=" CB CYS L 135 " ideal model delta sinusoidal sigma weight residual -86.00 -161.12 75.12 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS D 108 " pdb=" SG CYS D 108 " pdb=" SG CYS D 135 " pdb=" CB CYS D 135 " ideal model delta sinusoidal sigma weight residual -86.00 -141.67 55.67 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS H 108 " pdb=" SG CYS H 108 " pdb=" SG CYS H 135 " pdb=" CB CYS H 135 " ideal model delta sinusoidal sigma weight residual -86.00 -136.35 50.35 1 1.00e+01 1.00e-02 3.47e+01 ... (remaining 6981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1400 0.053 - 0.106: 288 0.106 - 0.159: 71 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 1762 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1759 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 40 " 0.093 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO I 41 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO I 41 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 41 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 276 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO J 277 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 277 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 277 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 49 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CG ASP D 49 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP D 49 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP D 49 " 0.011 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 302 2.68 - 3.24: 9554 3.24 - 3.79: 15313 3.79 - 4.35: 20454 4.35 - 4.90: 36480 Nonbonded interactions: 82103 Sorted by model distance: nonbonded pdb=" OG SER I 54 " pdb=" OE2 GLU K 564 " model vdw 2.130 3.040 nonbonded pdb=" N GLU F 318 " pdb=" OE1 GLU F 318 " model vdw 2.194 3.120 nonbonded pdb=" OG SER A 54 " pdb=" OE2 GLU C 564 " model vdw 2.196 3.040 nonbonded pdb=" O SER D 41 " pdb=" OG SER D 41 " model vdw 2.210 3.040 nonbonded pdb=" OG SER E 54 " pdb=" OE2 GLU G 564 " model vdw 2.212 3.040 ... (remaining 82098 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = (chain 'D' and resid 32 through 186) selection = (chain 'H' and resid 32 through 186) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.720 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.004 0.099 11558 Z= 0.170 Angle : 0.735 8.673 15712 Z= 0.382 Chirality : 0.046 0.265 1762 Planarity : 0.006 0.135 1984 Dihedral : 18.328 116.166 4324 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.48 % Favored : 94.10 % Rotamer: Outliers : 4.19 % Allowed : 27.72 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1423 helix: -0.48 (0.46), residues: 135 sheet: -0.37 (0.24), residues: 464 loop : -1.79 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 36 HIS 0.004 0.001 HIS A 35 PHE 0.010 0.001 PHE C 572 TYR 0.014 0.001 TYR L 99 ARG 0.015 0.001 ARG F 255 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00385 ( 3) link_ALPHA1-6 : angle 1.62757 ( 9) link_BETA1-4 : bond 0.00160 ( 6) link_BETA1-4 : angle 3.05738 ( 18) link_ALPHA1-3 : bond 0.00408 ( 3) link_ALPHA1-3 : angle 1.68550 ( 9) hydrogen bonds : bond 0.14233 ( 328) hydrogen bonds : angle 6.13161 ( 885) SS BOND : bond 0.00481 ( 18) SS BOND : angle 1.15694 ( 36) covalent geometry : bond 0.00354 (11528) covalent geometry : angle 0.72512 (15640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6533 (pt) REVERT: D 119 SER cc_start: 0.8313 (t) cc_final: 0.7665 (p) outliers start: 50 outliers final: 26 residues processed: 338 average time/residue: 1.1157 time to fit residues: 408.4834 Evaluate side-chains 193 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 65 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS D 107 ASN D 110 ASN E 116 GLN J 290 ASN K 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.110603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089090 restraints weight = 28997.571| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.25 r_work: 0.3500 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11558 Z= 0.143 Angle : 0.696 10.212 15712 Z= 0.353 Chirality : 0.045 0.179 1762 Planarity : 0.005 0.092 1984 Dihedral : 11.331 92.098 1904 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.69 % Favored : 94.10 % Rotamer: Outliers : 5.19 % Allowed : 28.39 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1423 helix: 0.36 (0.47), residues: 132 sheet: -0.22 (0.23), residues: 512 loop : -1.68 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 597 HIS 0.003 0.001 HIS H 139 PHE 0.012 0.001 PHE G 592 TYR 0.013 0.001 TYR I 80 ARG 0.007 0.001 ARG G 587 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00568 ( 3) link_ALPHA1-6 : angle 1.92464 ( 9) link_BETA1-4 : bond 0.00075 ( 6) link_BETA1-4 : angle 3.08745 ( 18) link_ALPHA1-3 : bond 0.01144 ( 3) link_ALPHA1-3 : angle 1.71837 ( 9) hydrogen bonds : bond 0.04613 ( 328) hydrogen bonds : angle 4.89670 ( 885) SS BOND : bond 0.00468 ( 18) SS BOND : angle 1.14505 ( 36) covalent geometry : bond 0.00316 (11528) covalent geometry : angle 0.68446 (15640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6551 (mm-30) REVERT: C 547 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8668 (tm) REVERT: D 110 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7610 (t0) REVERT: D 112 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6507 (tm-30) REVERT: E 46 GLU cc_start: 0.7765 (tt0) cc_final: 0.7515 (tt0) REVERT: E 116 GLN cc_start: 0.5327 (OUTLIER) cc_final: 0.5096 (pp30) REVERT: F 316 GLN cc_start: 0.8176 (tp40) cc_final: 0.7762 (mm-40) REVERT: F 339 LYS cc_start: 0.6898 (tppp) cc_final: 0.6572 (tppt) REVERT: H 56 LYS cc_start: 0.8021 (mptt) cc_final: 0.7605 (mptt) REVERT: H 78 ASP cc_start: 0.7532 (t0) cc_final: 0.7317 (t70) REVERT: H 156 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: I 19 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.6092 (ttt90) REVERT: L 119 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8062 (p) outliers start: 62 outliers final: 33 residues processed: 229 average time/residue: 1.3520 time to fit residues: 338.7491 Evaluate side-chains 188 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS C 560 GLN E 116 GLN J 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085661 restraints weight = 29526.120| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.28 r_work: 0.3436 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11558 Z= 0.195 Angle : 0.720 11.218 15712 Z= 0.365 Chirality : 0.046 0.185 1762 Planarity : 0.005 0.079 1984 Dihedral : 11.045 88.360 1892 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 6.28 % Allowed : 27.55 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1423 helix: 0.44 (0.48), residues: 132 sheet: 0.06 (0.23), residues: 507 loop : -1.88 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 114 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.002 PHE H 159 TYR 0.018 0.002 TYR E 57 ARG 0.010 0.001 ARG K 587 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00554 ( 3) link_ALPHA1-6 : angle 1.94869 ( 9) link_BETA1-4 : bond 0.00339 ( 6) link_BETA1-4 : angle 3.43366 ( 18) link_ALPHA1-3 : bond 0.00969 ( 3) link_ALPHA1-3 : angle 1.87617 ( 9) hydrogen bonds : bond 0.05422 ( 328) hydrogen bonds : angle 4.92949 ( 885) SS BOND : bond 0.00484 ( 18) SS BOND : angle 1.29226 ( 36) covalent geometry : bond 0.00449 (11528) covalent geometry : angle 0.70634 (15640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (pt) REVERT: C 550 ASN cc_start: 0.7074 (OUTLIER) cc_final: 0.6566 (t0) REVERT: D 112 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6527 (tm-30) REVERT: F 339 LYS cc_start: 0.6781 (tppp) cc_final: 0.6203 (tptt) REVERT: G 540 GLU cc_start: 0.8215 (pm20) cc_final: 0.7962 (pm20) REVERT: G 548 MET cc_start: 0.7854 (ttm) cc_final: 0.7565 (ttm) REVERT: H 56 LYS cc_start: 0.7930 (mptt) cc_final: 0.7569 (mptt) REVERT: H 59 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9003 (t) REVERT: H 64 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8219 (mmm160) REVERT: H 78 ASP cc_start: 0.7636 (t0) cc_final: 0.7366 (t70) REVERT: I 65 LYS cc_start: 0.9413 (tppp) cc_final: 0.8927 (tppp) REVERT: I 83 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7197 (pmm) REVERT: L 61 ASN cc_start: 0.8135 (m-40) cc_final: 0.7436 (p0) outliers start: 75 outliers final: 47 residues processed: 219 average time/residue: 1.2437 time to fit residues: 300.3389 Evaluate side-chains 201 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS C 595 GLN J 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.085405 restraints weight = 29350.081| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.27 r_work: 0.3423 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11558 Z= 0.174 Angle : 0.693 11.481 15712 Z= 0.349 Chirality : 0.045 0.154 1762 Planarity : 0.005 0.087 1984 Dihedral : 10.710 83.900 1892 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 6.70 % Allowed : 28.22 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1423 helix: 0.49 (0.48), residues: 132 sheet: 0.07 (0.23), residues: 507 loop : -1.87 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.006 0.001 HIS B 292 PHE 0.011 0.002 PHE I 29 TYR 0.015 0.002 TYR E 57 ARG 0.010 0.001 ARG A 14 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00499 ( 3) link_ALPHA1-6 : angle 1.86209 ( 9) link_BETA1-4 : bond 0.00337 ( 6) link_BETA1-4 : angle 3.22658 ( 18) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.90363 ( 9) hydrogen bonds : bond 0.05080 ( 328) hydrogen bonds : angle 4.93531 ( 885) SS BOND : bond 0.00466 ( 18) SS BOND : angle 1.22141 ( 36) covalent geometry : bond 0.00402 (11528) covalent geometry : angle 0.68092 (15640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 550 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6706 (t0) REVERT: C 558 LEU cc_start: 0.8526 (tt) cc_final: 0.8283 (tp) REVERT: C 596 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7446 (tpm170) REVERT: D 112 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6678 (tm-30) REVERT: F 316 GLN cc_start: 0.8215 (tp40) cc_final: 0.7943 (mm-40) REVERT: F 341 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7102 (mm-30) REVERT: G 503 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7663 (m) REVERT: G 510 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6669 (ptpp) REVERT: G 540 GLU cc_start: 0.8352 (pm20) cc_final: 0.8052 (pm20) REVERT: H 56 LYS cc_start: 0.8066 (mptt) cc_final: 0.7666 (mptt) REVERT: H 59 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9056 (t) REVERT: H 64 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7441 (mmm160) REVERT: H 78 ASP cc_start: 0.7823 (t0) cc_final: 0.7524 (OUTLIER) REVERT: I 19 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6104 (ttt-90) REVERT: I 65 LYS cc_start: 0.9443 (tppp) cc_final: 0.8926 (tppp) REVERT: I 83 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7195 (pmm) REVERT: I 89 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: L 61 ASN cc_start: 0.8345 (m-40) cc_final: 0.7664 (p0) REVERT: L 115 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8180 (mmmt) outliers start: 80 outliers final: 53 residues processed: 225 average time/residue: 1.0380 time to fit residues: 256.0186 Evaluate side-chains 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS C 595 GLN J 290 ASN L 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.107635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.086129 restraints weight = 29043.764| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.25 r_work: 0.3452 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11558 Z= 0.131 Angle : 0.646 9.759 15712 Z= 0.324 Chirality : 0.044 0.158 1762 Planarity : 0.005 0.080 1984 Dihedral : 9.868 77.677 1891 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 6.03 % Allowed : 28.98 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1423 helix: 0.46 (0.47), residues: 132 sheet: 0.02 (0.23), residues: 513 loop : -1.77 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.002 0.001 HIS D 139 PHE 0.010 0.001 PHE G 592 TYR 0.014 0.001 TYR A 94 ARG 0.009 0.001 ARG G 587 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00608 ( 3) link_ALPHA1-6 : angle 1.76185 ( 9) link_BETA1-4 : bond 0.00100 ( 6) link_BETA1-4 : angle 2.69040 ( 18) link_ALPHA1-3 : bond 0.01163 ( 3) link_ALPHA1-3 : angle 1.48478 ( 9) hydrogen bonds : bond 0.04266 ( 328) hydrogen bonds : angle 4.80963 ( 885) SS BOND : bond 0.00397 ( 18) SS BOND : angle 1.07656 ( 36) covalent geometry : bond 0.00294 (11528) covalent geometry : angle 0.63609 (15640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 LEU cc_start: 0.8179 (tp) cc_final: 0.7928 (mp) REVERT: B 319 ASP cc_start: 0.7230 (m-30) cc_final: 0.6562 (p0) REVERT: B 341 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6526 (mm-30) REVERT: C 558 LEU cc_start: 0.8484 (tt) cc_final: 0.8214 (tp) REVERT: C 596 ARG cc_start: 0.8121 (ttt90) cc_final: 0.7547 (tpm170) REVERT: D 112 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 316 GLN cc_start: 0.8256 (tp40) cc_final: 0.7799 (mm-40) REVERT: F 339 LYS cc_start: 0.6942 (tppp) cc_final: 0.6047 (tptt) REVERT: G 503 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7777 (m) REVERT: G 510 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6799 (ptpp) REVERT: G 540 GLU cc_start: 0.8358 (pm20) cc_final: 0.8148 (pm20) REVERT: G 592 PHE cc_start: 0.8515 (t80) cc_final: 0.8293 (t80) REVERT: H 56 LYS cc_start: 0.8098 (mptt) cc_final: 0.7746 (mptt) REVERT: H 59 SER cc_start: 0.9379 (m) cc_final: 0.9094 (t) REVERT: H 78 ASP cc_start: 0.7892 (t0) cc_final: 0.7610 (OUTLIER) REVERT: I 65 LYS cc_start: 0.9477 (tppp) cc_final: 0.8959 (tppp) REVERT: I 83 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7004 (pmm) REVERT: I 89 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: K 508 GLN cc_start: 0.6840 (mp10) cc_final: 0.6635 (mp10) REVERT: L 61 ASN cc_start: 0.8259 (m-40) cc_final: 0.7686 (p0) outliers start: 72 outliers final: 49 residues processed: 225 average time/residue: 0.9119 time to fit residues: 226.3675 Evaluate side-chains 205 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 508 GLN C 595 GLN J 290 ASN ** J 336 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 = 0.3933 r_free = 0.3933 target = 0.105035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.083677 restraints weight = 29594.098| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.21 r_work: 0.3407 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11558 Z= 0.186 Angle : 0.707 9.473 15712 Z= 0.357 Chirality : 0.046 0.148 1762 Planarity : 0.005 0.079 1984 Dihedral : 9.811 75.407 1889 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.15 % Favored : 91.71 % Rotamer: Outliers : 6.53 % Allowed : 28.48 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1423 helix: 0.33 (0.47), residues: 132 sheet: 0.08 (0.23), residues: 504 loop : -1.94 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 272 HIS 0.003 0.001 HIS H 139 PHE 0.015 0.002 PHE I 29 TYR 0.017 0.002 TYR E 57 ARG 0.011 0.001 ARG G 587 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00629 ( 3) link_ALPHA1-6 : angle 1.67522 ( 9) link_BETA1-4 : bond 0.00312 ( 6) link_BETA1-4 : angle 3.19111 ( 18) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 2.13246 ( 9) hydrogen bonds : bond 0.05263 ( 328) hydrogen bonds : angle 4.91896 ( 885) SS BOND : bond 0.00486 ( 18) SS BOND : angle 1.27368 ( 36) covalent geometry : bond 0.00429 (11528) covalent geometry : angle 0.69484 (15640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6863 (mtm-85) cc_final: 0.6418 (ptp-110) REVERT: B 319 ASP cc_start: 0.7225 (m-30) cc_final: 0.6658 (p0) REVERT: C 558 LEU cc_start: 0.8535 (tt) cc_final: 0.8264 (tp) REVERT: C 596 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7504 (tpm170) REVERT: D 112 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6923 (tm-30) REVERT: F 316 GLN cc_start: 0.8323 (tp40) cc_final: 0.8007 (mm-40) REVERT: G 503 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7744 (m) REVERT: G 540 GLU cc_start: 0.8374 (pm20) cc_final: 0.8128 (pm20) REVERT: G 592 PHE cc_start: 0.8627 (t80) cc_final: 0.8341 (t80) REVERT: H 56 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7700 (mptt) REVERT: H 59 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9117 (t) REVERT: H 78 ASP cc_start: 0.8002 (t0) cc_final: 0.7726 (t70) REVERT: I 19 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6234 (ttt-90) REVERT: I 83 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7064 (pmm) REVERT: I 89 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: L 56 LYS cc_start: 0.8056 (mppt) cc_final: 0.7553 (mppt) REVERT: L 61 ASN cc_start: 0.8284 (m-40) cc_final: 0.7767 (p0) outliers start: 78 outliers final: 55 residues processed: 221 average time/residue: 0.9248 time to fit residues: 226.1633 Evaluate side-chains 210 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS C 508 GLN C 595 GLN J 290 ASN L 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.107291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085951 restraints weight = 29259.328| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 4.23 r_work: 0.3453 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11558 Z= 0.126 Angle : 0.658 8.614 15712 Z= 0.333 Chirality : 0.044 0.180 1762 Planarity : 0.005 0.080 1984 Dihedral : 9.219 68.666 1889 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.55 % Favored : 94.31 % Rotamer: Outliers : 4.44 % Allowed : 30.82 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1423 helix: 0.33 (0.46), residues: 132 sheet: 0.02 (0.24), residues: 515 loop : -1.81 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 104 HIS 0.002 0.001 HIS D 139 PHE 0.011 0.001 PHE J 320 TYR 0.017 0.001 TYR A 94 ARG 0.011 0.001 ARG G 587 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 1.60661 ( 9) link_BETA1-4 : bond 0.00222 ( 6) link_BETA1-4 : angle 2.47154 ( 18) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.25517 ( 9) hydrogen bonds : bond 0.04004 ( 328) hydrogen bonds : angle 4.81180 ( 885) SS BOND : bond 0.00378 ( 18) SS BOND : angle 1.00067 ( 36) covalent geometry : bond 0.00278 (11528) covalent geometry : angle 0.65090 (15640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ASP cc_start: 0.7226 (m-30) cc_final: 0.6597 (p0) REVERT: B 341 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6550 (mm-30) REVERT: C 558 LEU cc_start: 0.8483 (tt) cc_final: 0.8210 (tp) REVERT: C 596 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7561 (tpm170) REVERT: D 112 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6836 (tm-30) REVERT: F 261 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7819 (tpp80) REVERT: F 316 GLN cc_start: 0.8390 (tp40) cc_final: 0.7941 (mm-40) REVERT: F 339 LYS cc_start: 0.6974 (tppp) cc_final: 0.6681 (tppt) REVERT: G 540 GLU cc_start: 0.8308 (pm20) cc_final: 0.8052 (pm20) REVERT: G 592 PHE cc_start: 0.8616 (t80) cc_final: 0.8309 (t80) REVERT: H 56 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7729 (mptt) REVERT: H 59 SER cc_start: 0.9348 (m) cc_final: 0.9074 (t) REVERT: H 78 ASP cc_start: 0.7954 (t0) cc_final: 0.7688 (t70) REVERT: I 19 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6153 (ttt-90) REVERT: I 83 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6984 (pmm) REVERT: I 89 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: L 61 ASN cc_start: 0.8199 (m-40) cc_final: 0.7736 (p0) outliers start: 53 outliers final: 44 residues processed: 211 average time/residue: 1.0999 time to fit residues: 254.5245 Evaluate side-chains 204 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 508 GLN J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083478 restraints weight = 29657.651| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.22 r_work: 0.3406 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11558 Z= 0.186 Angle : 0.731 9.620 15712 Z= 0.368 Chirality : 0.046 0.166 1762 Planarity : 0.005 0.084 1984 Dihedral : 9.207 67.695 1888 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.78 % Rotamer: Outliers : 5.44 % Allowed : 30.65 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.22), residues: 1423 helix: 0.07 (0.45), residues: 132 sheet: 0.10 (0.24), residues: 501 loop : -1.94 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 272 HIS 0.003 0.001 HIS I 35 PHE 0.017 0.002 PHE I 29 TYR 0.017 0.002 TYR E 57 ARG 0.011 0.001 ARG D 136 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00776 ( 3) link_ALPHA1-6 : angle 1.47706 ( 9) link_BETA1-4 : bond 0.00299 ( 6) link_BETA1-4 : angle 3.04471 ( 18) link_ALPHA1-3 : bond 0.00844 ( 3) link_ALPHA1-3 : angle 2.26932 ( 9) hydrogen bonds : bond 0.05224 ( 328) hydrogen bonds : angle 4.95150 ( 885) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.18417 ( 36) covalent geometry : bond 0.00431 (11528) covalent geometry : angle 0.72036 (15640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6575 (tp) REVERT: B 319 ASP cc_start: 0.7106 (m-30) cc_final: 0.6706 (p0) REVERT: C 558 LEU cc_start: 0.8620 (tt) cc_final: 0.8397 (tp) REVERT: C 596 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7515 (tpm170) REVERT: D 112 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6956 (tm-30) REVERT: F 261 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7910 (tpp80) REVERT: F 316 GLN cc_start: 0.8317 (tp40) cc_final: 0.8031 (mm-40) REVERT: F 339 LYS cc_start: 0.7362 (tppp) cc_final: 0.6469 (tptt) REVERT: G 503 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7769 (m) REVERT: G 540 GLU cc_start: 0.8425 (pm20) cc_final: 0.8150 (pm20) REVERT: G 592 PHE cc_start: 0.8722 (t80) cc_final: 0.8491 (t80) REVERT: H 56 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7807 (mptt) REVERT: H 59 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9108 (t) REVERT: H 78 ASP cc_start: 0.7976 (t0) cc_final: 0.7708 (t70) REVERT: I 19 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6046 (ptm160) REVERT: I 83 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7052 (pmm) REVERT: I 89 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: L 61 ASN cc_start: 0.8164 (m-40) cc_final: 0.7746 (p0) REVERT: L 115 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7983 (mmmt) outliers start: 65 outliers final: 49 residues processed: 211 average time/residue: 0.9936 time to fit residues: 230.7494 Evaluate side-chains 208 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS J 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.107034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085663 restraints weight = 29514.438| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.25 r_work: 0.3452 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11558 Z= 0.130 Angle : 0.690 10.449 15712 Z= 0.346 Chirality : 0.045 0.270 1762 Planarity : 0.005 0.081 1984 Dihedral : 8.611 61.994 1888 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 4.02 % Allowed : 32.24 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1423 helix: 0.01 (0.44), residues: 138 sheet: 0.04 (0.24), residues: 511 loop : -1.83 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 272 HIS 0.003 0.001 HIS H 139 PHE 0.011 0.001 PHE J 320 TYR 0.011 0.001 TYR H 99 ARG 0.016 0.001 ARG A 87 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00875 ( 3) link_ALPHA1-6 : angle 1.54624 ( 9) link_BETA1-4 : bond 0.00240 ( 6) link_BETA1-4 : angle 2.47026 ( 18) link_ALPHA1-3 : bond 0.01358 ( 3) link_ALPHA1-3 : angle 1.35588 ( 9) hydrogen bonds : bond 0.04012 ( 328) hydrogen bonds : angle 4.83694 ( 885) SS BOND : bond 0.00370 ( 18) SS BOND : angle 0.98582 ( 36) covalent geometry : bond 0.00291 (11528) covalent geometry : angle 0.68328 (15640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6493 (tp) REVERT: B 319 ASP cc_start: 0.7204 (m-30) cc_final: 0.6651 (p0) REVERT: B 341 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6547 (mm-30) REVERT: C 558 LEU cc_start: 0.8557 (tt) cc_final: 0.8280 (tp) REVERT: C 596 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7539 (tpm170) REVERT: D 112 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6868 (tm-30) REVERT: F 261 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7871 (tpp80) REVERT: F 316 GLN cc_start: 0.8387 (tp40) cc_final: 0.8147 (mm-40) REVERT: F 339 LYS cc_start: 0.7378 (tppp) cc_final: 0.6484 (tptt) REVERT: G 540 GLU cc_start: 0.8295 (pm20) cc_final: 0.8091 (pm20) REVERT: G 592 PHE cc_start: 0.8659 (t80) cc_final: 0.8367 (t80) REVERT: G 596 ARG cc_start: 0.7876 (tmm160) cc_final: 0.7568 (tmm160) REVERT: H 56 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7729 (mppt) REVERT: H 59 SER cc_start: 0.9331 (m) cc_final: 0.9068 (t) REVERT: H 78 ASP cc_start: 0.8029 (t0) cc_final: 0.7808 (t0) REVERT: I 19 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5998 (ptm160) REVERT: I 83 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6973 (pmm) REVERT: I 89 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: L 61 ASN cc_start: 0.8166 (m-40) cc_final: 0.7746 (p0) REVERT: L 115 LYS cc_start: 0.8241 (mmmt) cc_final: 0.8017 (mmmt) outliers start: 48 outliers final: 42 residues processed: 205 average time/residue: 0.9910 time to fit residues: 222.9387 Evaluate side-chains 204 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 586 ASN Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.104889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083754 restraints weight = 29254.239| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.22 r_work: 0.3412 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11558 Z= 0.180 Angle : 0.740 12.566 15712 Z= 0.372 Chirality : 0.046 0.197 1762 Planarity : 0.006 0.082 1984 Dihedral : 8.610 62.739 1887 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.92 % Rotamer: Outliers : 4.36 % Allowed : 32.33 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1423 helix: -0.02 (0.44), residues: 132 sheet: 0.08 (0.24), residues: 506 loop : -1.95 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 47 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.002 PHE I 29 TYR 0.017 0.002 TYR A 94 ARG 0.022 0.001 ARG A 87 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00931 ( 3) link_ALPHA1-6 : angle 1.36427 ( 9) link_BETA1-4 : bond 0.00277 ( 6) link_BETA1-4 : angle 2.91942 ( 18) link_ALPHA1-3 : bond 0.00897 ( 3) link_ALPHA1-3 : angle 2.11289 ( 9) hydrogen bonds : bond 0.05031 ( 328) hydrogen bonds : angle 4.93530 ( 885) SS BOND : bond 0.00448 ( 18) SS BOND : angle 1.15674 ( 36) covalent geometry : bond 0.00417 (11528) covalent geometry : angle 0.73023 (15640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6410 (tp) REVERT: B 319 ASP cc_start: 0.7079 (m-30) cc_final: 0.6707 (p0) REVERT: C 558 LEU cc_start: 0.8593 (tt) cc_final: 0.8331 (tp) REVERT: C 596 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7487 (tpm170) REVERT: D 112 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6857 (tm-30) REVERT: D 136 ARG cc_start: 0.7279 (mmp80) cc_final: 0.7072 (mmp80) REVERT: F 261 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7922 (tpp80) REVERT: F 290 ASN cc_start: 0.8607 (m-40) cc_final: 0.7968 (p0) REVERT: F 316 GLN cc_start: 0.8388 (tp40) cc_final: 0.8060 (mm-40) REVERT: F 339 LYS cc_start: 0.7401 (tppp) cc_final: 0.6497 (tptt) REVERT: G 503 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7743 (m) REVERT: G 540 GLU cc_start: 0.8362 (pm20) cc_final: 0.8137 (pm20) REVERT: G 592 PHE cc_start: 0.8622 (t80) cc_final: 0.8358 (t80) REVERT: G 596 ARG cc_start: 0.7836 (tmm160) cc_final: 0.7590 (tmm160) REVERT: H 55 ASP cc_start: 0.8657 (m-30) cc_final: 0.8402 (p0) REVERT: H 56 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7756 (mptt) REVERT: H 59 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9088 (t) REVERT: H 78 ASP cc_start: 0.8066 (t0) cc_final: 0.7845 (t0) REVERT: I 19 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6026 (ptm160) REVERT: I 83 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7018 (pmm) REVERT: I 89 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: L 61 ASN cc_start: 0.8203 (m-40) cc_final: 0.7766 (p0) outliers start: 52 outliers final: 40 residues processed: 202 average time/residue: 0.9764 time to fit residues: 216.8783 Evaluate side-chains 204 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 chunk 42 optimal weight: 0.0050 chunk 107 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS J 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086440 restraints weight = 28685.134| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.18 r_work: 0.3468 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11558 Z= 0.127 Angle : 0.695 12.522 15712 Z= 0.347 Chirality : 0.045 0.214 1762 Planarity : 0.005 0.082 1984 Dihedral : 8.059 56.663 1887 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 4.10 % Allowed : 33.00 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.22), residues: 1423 helix: -0.05 (0.44), residues: 138 sheet: 0.06 (0.24), residues: 501 loop : -1.81 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 272 HIS 0.003 0.001 HIS H 139 PHE 0.011 0.001 PHE J 320 TYR 0.012 0.001 TYR L 137 ARG 0.019 0.001 ARG A 87 Details of bonding type rmsd link_ALPHA1-6 : bond 0.00970 ( 3) link_ALPHA1-6 : angle 1.55229 ( 9) link_BETA1-4 : bond 0.00270 ( 6) link_BETA1-4 : angle 2.33278 ( 18) link_ALPHA1-3 : bond 0.01281 ( 3) link_ALPHA1-3 : angle 1.12352 ( 9) hydrogen bonds : bond 0.03808 ( 328) hydrogen bonds : angle 4.81867 ( 885) SS BOND : bond 0.00357 ( 18) SS BOND : angle 0.95679 ( 36) covalent geometry : bond 0.00288 (11528) covalent geometry : angle 0.68894 (15640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8910.49 seconds wall clock time: 155 minutes 36.48 seconds (9336.48 seconds total)