Starting phenix.real_space_refine on Wed Sep 17 20:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3u_38899/09_2025/8y3u_38899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3u_38899/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y3u_38899/09_2025/8y3u_38899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3u_38899/09_2025/8y3u_38899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3u_38899/09_2025/8y3u_38899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3u_38899/09_2025/8y3u_38899.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: 3.20, per 1000 atoms: 0.28 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: 1.25 Conformation dependent library (CDL) restraints added in 449.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.47 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: 1.75 Time building geometry restraints manager: 1.62 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: 5.590 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (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 ARG 0.015 0.001 ARG F 255 TYR 0.014 0.001 TYR L 99 PHE 0.010 0.001 PHE C 572 TRP 0.013 0.001 TRP I 36 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00354 (11528) covalent geometry : angle 0.72512 (15640) SS BOND : bond 0.00481 ( 18) SS BOND : angle 1.15694 ( 36) hydrogen bonds : bond 0.14233 ( 328) hydrogen bonds : angle 6.13161 ( 885) link_ALPHA1-3 : bond 0.00408 ( 3) link_ALPHA1-3 : angle 1.68550 ( 9) 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) *********************** 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 : 0.452 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: 0.7669 (p) outliers start: 50 outliers final: 26 residues processed: 338 average time/residue: 0.5576 time to fit residues: 203.3712 Evaluate side-chains 191 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.088437 restraints weight = 29350.179| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.28 r_work: 0.3489 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11558 Z= 0.149 Angle : 0.712 10.641 15712 Z= 0.359 Chirality : 0.046 0.178 1762 Planarity : 0.005 0.091 1984 Dihedral : 11.146 90.063 1904 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 6.03 % Allowed : 27.47 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.22), residues: 1423 helix: 0.30 (0.47), residues: 132 sheet: -0.23 (0.23), residues: 512 loop : -1.69 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.014 0.001 TYR I 80 PHE 0.012 0.001 PHE G 592 TRP 0.014 0.001 TRP K 597 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00336 (11528) covalent geometry : angle 0.70021 (15640) SS BOND : bond 0.00476 ( 18) SS BOND : angle 1.18784 ( 36) hydrogen bonds : bond 0.04616 ( 328) hydrogen bonds : angle 4.86688 ( 885) link_ALPHA1-3 : bond 0.01360 ( 3) link_ALPHA1-3 : angle 2.00073 ( 9) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.81708 ( 9) link_BETA1-4 : bond 0.00127 ( 6) link_BETA1-4 : angle 3.24068 ( 18) *********************** 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 247 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6635 (mm-30) REVERT: C 547 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (tm) REVERT: D 110 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7654 (t0) REVERT: D 112 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6526 (tm-30) REVERT: E 116 GLN cc_start: 0.5664 (OUTLIER) cc_final: 0.5382 (pp30) REVERT: F 282 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8403 (mtmt) REVERT: F 316 GLN cc_start: 0.8239 (tp40) cc_final: 0.7840 (mm-40) REVERT: F 339 LYS cc_start: 0.6941 (tppp) cc_final: 0.6640 (tppt) REVERT: H 56 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7768 (mptt) REVERT: H 78 ASP cc_start: 0.7605 (t0) cc_final: 0.7344 (t70) REVERT: I 19 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6112 (ttt90) REVERT: L 119 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8084 (p) REVERT: L 129 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6512 (tp) outliers start: 72 outliers final: 32 residues processed: 229 average time/residue: 0.5333 time to fit residues: 132.2863 Evaluate side-chains 188 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL 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 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 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 129 ILE Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 E 116 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 = 0.3988 r_free = 0.3988 target = 0.108637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087183 restraints weight = 29232.096| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.26 r_work: 0.3458 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11558 Z= 0.158 Angle : 0.678 10.773 15712 Z= 0.343 Chirality : 0.044 0.181 1762 Planarity : 0.005 0.081 1984 Dihedral : 10.757 86.838 1892 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.32 % Rotamer: Outliers : 6.20 % Allowed : 27.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.22), residues: 1423 helix: 0.51 (0.48), residues: 132 sheet: -0.15 (0.23), residues: 528 loop : -1.68 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 587 TYR 0.014 0.001 TYR A 94 PHE 0.015 0.002 PHE F 320 TRP 0.015 0.002 TRP E 114 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00359 (11528) covalent geometry : angle 0.66592 (15640) SS BOND : bond 0.00433 ( 18) SS BOND : angle 1.16331 ( 36) hydrogen bonds : bond 0.04830 ( 328) hydrogen bonds : angle 4.86217 ( 885) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 1.70251 ( 9) link_ALPHA1-6 : bond 0.00573 ( 3) link_ALPHA1-6 : angle 1.85338 ( 9) link_BETA1-4 : bond 0.00134 ( 6) link_BETA1-4 : angle 3.10833 ( 18) *********************** 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 239 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 165 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: D 112 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6539 (tm-30) REVERT: D 185 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7427 (pp) REVERT: G 540 GLU cc_start: 0.8179 (pm20) cc_final: 0.7925 (pm20) REVERT: H 56 LYS cc_start: 0.7979 (mptt) cc_final: 0.7629 (mptt) REVERT: H 59 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8992 (t) REVERT: H 64 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7328 (mmm160) REVERT: H 78 ASP cc_start: 0.7725 (t0) cc_final: 0.7402 (t70) REVERT: I 19 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.6066 (ttt-90) REVERT: I 65 LYS cc_start: 0.9413 (tppp) cc_final: 0.9009 (tppp) REVERT: I 83 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7286 (pmm) REVERT: L 61 ASN cc_start: 0.8124 (m-40) cc_final: 0.7397 (p0) outliers start: 74 outliers final: 46 residues processed: 217 average time/residue: 0.4814 time to fit residues: 114.3703 Evaluate side-chains 202 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain B residue 282 LYS 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 D residue 185 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 110 ASN J 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.108337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086828 restraints weight = 29245.319| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.25 r_work: 0.3450 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11558 Z= 0.144 Angle : 0.662 10.954 15712 Z= 0.332 Chirality : 0.045 0.156 1762 Planarity : 0.005 0.075 1984 Dihedral : 10.169 80.196 1892 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 5.78 % Allowed : 28.14 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.22), residues: 1423 helix: 0.46 (0.47), residues: 132 sheet: 0.05 (0.23), residues: 513 loop : -1.72 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 587 TYR 0.015 0.001 TYR A 94 PHE 0.015 0.001 PHE L 151 TRP 0.008 0.001 TRP I 36 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00326 (11528) covalent geometry : angle 0.65144 (15640) SS BOND : bond 0.00436 ( 18) SS BOND : angle 1.12874 ( 36) hydrogen bonds : bond 0.04543 ( 328) hydrogen bonds : angle 4.80908 ( 885) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 1.59418 ( 9) link_ALPHA1-6 : bond 0.00611 ( 3) link_ALPHA1-6 : angle 1.85645 ( 9) link_BETA1-4 : bond 0.00179 ( 6) link_BETA1-4 : angle 2.94396 ( 18) *********************** 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 238 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 169 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6722 (mm-30) REVERT: C 596 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7518 (tpm170) REVERT: D 112 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6623 (tm-30) REVERT: F 339 LYS cc_start: 0.6770 (tppp) cc_final: 0.6357 (tppt) REVERT: G 503 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7673 (m) REVERT: G 540 GLU cc_start: 0.8297 (pm20) cc_final: 0.8012 (pm20) REVERT: H 56 LYS cc_start: 0.8012 (mptt) cc_final: 0.7582 (mptt) REVERT: H 59 SER cc_start: 0.9328 (m) cc_final: 0.9023 (t) REVERT: H 78 ASP cc_start: 0.7890 (t0) cc_final: 0.7531 (t70) REVERT: I 65 LYS cc_start: 0.9424 (tppp) cc_final: 0.8918 (tppp) REVERT: I 80 TYR cc_start: 0.7711 (m-80) cc_final: 0.7473 (m-80) REVERT: I 83 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7208 (pmm) REVERT: I 89 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: L 61 ASN cc_start: 0.8277 (m-40) cc_final: 0.7648 (p0) outliers start: 69 outliers final: 48 residues processed: 219 average time/residue: 0.4667 time to fit residues: 112.0145 Evaluate side-chains 204 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 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 83 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 18 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 86 LEU 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 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 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 184 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 42 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.106719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085286 restraints weight = 29190.540| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.23 r_work: 0.3432 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11558 Z= 0.166 Angle : 0.683 11.638 15712 Z= 0.344 Chirality : 0.045 0.154 1762 Planarity : 0.005 0.073 1984 Dihedral : 9.997 77.786 1889 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 6.28 % Allowed : 28.22 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.22), residues: 1423 helix: 0.44 (0.47), residues: 132 sheet: -0.02 (0.23), residues: 513 loop : -1.78 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 14 TYR 0.015 0.001 TYR E 57 PHE 0.012 0.002 PHE I 29 TRP 0.008 0.001 TRP E 36 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00385 (11528) covalent geometry : angle 0.67162 (15640) SS BOND : bond 0.00440 ( 18) SS BOND : angle 1.15868 ( 36) hydrogen bonds : bond 0.04874 ( 328) hydrogen bonds : angle 4.85792 ( 885) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.82857 ( 9) link_ALPHA1-6 : bond 0.00605 ( 3) link_ALPHA1-6 : angle 1.80668 ( 9) link_BETA1-4 : bond 0.00221 ( 6) link_BETA1-4 : angle 3.04702 ( 18) *********************** 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 241 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 166 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7717 (ptp-110) REVERT: B 319 ASP cc_start: 0.7237 (m-30) cc_final: 0.6561 (p0) REVERT: C 558 LEU cc_start: 0.8495 (tt) cc_final: 0.8288 (tp) REVERT: C 596 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7532 (tpm170) REVERT: D 112 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6811 (tm-30) REVERT: F 261 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7846 (tpp80) REVERT: F 316 GLN cc_start: 0.8240 (tp40) cc_final: 0.8028 (mm-40) REVERT: F 339 LYS cc_start: 0.6906 (tppp) cc_final: 0.6374 (tppt) REVERT: G 503 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7772 (m) REVERT: G 540 GLU cc_start: 0.8387 (pm20) cc_final: 0.8158 (pm20) REVERT: G 592 PHE cc_start: 0.8526 (t80) cc_final: 0.8314 (t80) REVERT: H 56 LYS cc_start: 0.8058 (mptt) cc_final: 0.7661 (mptt) REVERT: H 59 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9098 (t) REVERT: H 78 ASP cc_start: 0.7952 (t0) cc_final: 0.7642 (t70) REVERT: I 65 LYS cc_start: 0.9473 (tppp) cc_final: 0.8950 (tppp) REVERT: I 80 TYR cc_start: 0.7768 (m-80) cc_final: 0.7509 (m-80) REVERT: I 83 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7263 (pmm) REVERT: I 89 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: L 61 ASN cc_start: 0.8267 (m-40) cc_final: 0.7677 (p0) outliers start: 75 outliers final: 52 residues processed: 221 average time/residue: 0.4588 time to fit residues: 111.3591 Evaluate side-chains 207 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 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 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 83 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 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 63 SER 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 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 59 SER 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 28 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 55 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 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.108301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.086704 restraints weight = 29101.628| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.24 r_work: 0.3466 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11558 Z= 0.125 Angle : 0.644 10.396 15712 Z= 0.327 Chirality : 0.044 0.185 1762 Planarity : 0.005 0.079 1984 Dihedral : 9.193 70.722 1889 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.69 % Favored : 94.17 % Rotamer: Outliers : 5.36 % Allowed : 29.48 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.22), residues: 1423 helix: 0.53 (0.47), residues: 132 sheet: 0.11 (0.24), residues: 479 loop : -1.72 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 587 TYR 0.019 0.001 TYR A 80 PHE 0.009 0.001 PHE J 320 TRP 0.006 0.001 TRP I 36 HIS 0.003 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00278 (11528) covalent geometry : angle 0.63575 (15640) SS BOND : bond 0.00385 ( 18) SS BOND : angle 1.01915 ( 36) hydrogen bonds : bond 0.03968 ( 328) hydrogen bonds : angle 4.73578 ( 885) link_ALPHA1-3 : bond 0.01224 ( 3) link_ALPHA1-3 : angle 1.32563 ( 9) link_ALPHA1-6 : bond 0.00758 ( 3) link_ALPHA1-6 : angle 1.76567 ( 9) link_BETA1-4 : bond 0.00146 ( 6) link_BETA1-4 : angle 2.52760 ( 18) *********************** 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 234 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ASP cc_start: 0.7172 (m-30) cc_final: 0.6505 (p0) REVERT: B 341 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6462 (mm-30) REVERT: C 558 LEU cc_start: 0.8424 (tt) cc_final: 0.8130 (tp) REVERT: C 596 ARG cc_start: 0.8206 (ttt90) cc_final: 0.7571 (tpm170) REVERT: D 112 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6700 (tm-30) REVERT: F 261 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7797 (tpp80) REVERT: F 316 GLN cc_start: 0.8292 (tp40) cc_final: 0.7795 (mm-40) REVERT: F 339 LYS cc_start: 0.6959 (tppp) cc_final: 0.6585 (tppt) REVERT: G 540 GLU cc_start: 0.8305 (pm20) cc_final: 0.8055 (pm20) REVERT: G 576 THR cc_start: 0.7013 (m) cc_final: 0.6805 (t) REVERT: G 592 PHE cc_start: 0.8558 (t80) cc_final: 0.8232 (t80) REVERT: H 56 LYS cc_start: 0.8099 (mptt) cc_final: 0.7714 (mptt) REVERT: H 59 SER cc_start: 0.9370 (m) cc_final: 0.9099 (t) REVERT: H 64 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8295 (mmm160) REVERT: H 78 ASP cc_start: 0.7964 (t0) cc_final: 0.7639 (t70) REVERT: I 80 TYR cc_start: 0.7697 (m-80) cc_final: 0.7472 (m-80) REVERT: I 83 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7149 (pmm) REVERT: I 89 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: I 100 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7563 (ptm) REVERT: L 61 ASN cc_start: 0.8219 (m-40) cc_final: 0.7666 (p0) REVERT: L 115 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7940 (mmmt) outliers start: 64 outliers final: 44 residues processed: 218 average time/residue: 0.5080 time to fit residues: 120.3891 Evaluate side-chains 197 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR 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 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 588 LYS 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 53 SER Chi-restraints excluded: chain E residue 86 LEU 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 297 SER Chi-restraints excluded: chain F residue 322 THR 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 136 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 58 LYS 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 I residue 100 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 595 GLN J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.105875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.084466 restraints weight = 29336.646| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.20 r_work: 0.3422 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11558 Z= 0.170 Angle : 0.704 10.029 15712 Z= 0.354 Chirality : 0.046 0.174 1762 Planarity : 0.005 0.080 1984 Dihedral : 9.110 68.924 1889 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.92 % Rotamer: Outliers : 5.61 % Allowed : 30.15 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.22), residues: 1423 helix: 0.33 (0.46), residues: 132 sheet: 0.07 (0.24), residues: 477 loop : -1.83 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 136 TYR 0.018 0.001 TYR A 80 PHE 0.015 0.002 PHE I 29 TRP 0.008 0.001 TRP I 36 HIS 0.004 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00390 (11528) covalent geometry : angle 0.69337 (15640) SS BOND : bond 0.00456 ( 18) SS BOND : angle 1.13743 ( 36) hydrogen bonds : bond 0.04916 ( 328) hydrogen bonds : angle 4.82621 ( 885) link_ALPHA1-3 : bond 0.00675 ( 3) link_ALPHA1-3 : angle 1.84255 ( 9) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 1.66282 ( 9) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 2.96527 ( 18) *********************** 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 232 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ASP cc_start: 0.7202 (m-30) cc_final: 0.6655 (p0) REVERT: C 558 LEU cc_start: 0.8522 (tt) cc_final: 0.8190 (tp) REVERT: C 596 ARG cc_start: 0.8267 (ttt90) cc_final: 0.7565 (tpm170) REVERT: D 112 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6876 (tm-30) REVERT: F 261 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7752 (tpp80) REVERT: F 316 GLN cc_start: 0.8259 (tp40) cc_final: 0.7932 (mm-40) REVERT: G 503 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7780 (m) REVERT: G 540 GLU cc_start: 0.8336 (pm20) cc_final: 0.8101 (pm20) REVERT: G 592 PHE cc_start: 0.8667 (t80) cc_final: 0.8360 (t80) REVERT: H 56 LYS cc_start: 0.8096 (mptt) cc_final: 0.7702 (mptt) REVERT: H 59 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9115 (t) REVERT: H 78 ASP cc_start: 0.8059 (t0) cc_final: 0.7752 (t70) REVERT: I 80 TYR cc_start: 0.7803 (m-80) cc_final: 0.7536 (m-80) REVERT: I 83 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7247 (pmm) REVERT: I 89 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: L 56 LYS cc_start: 0.8110 (mppt) cc_final: 0.7558 (mppt) REVERT: L 61 ASN cc_start: 0.8167 (m-40) cc_final: 0.7723 (p0) REVERT: L 115 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8147 (mmtt) outliers start: 67 outliers final: 53 residues processed: 212 average time/residue: 0.4689 time to fit residues: 108.4898 Evaluate side-chains 210 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 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 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 588 LYS 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 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 H residue 55 ASP 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 184 LEU 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 55 SER Chi-restraints excluded: chain I residue 58 LYS 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 184 LEU 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 33 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 595 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 = 0.3972 r_free = 0.3972 target = 0.107237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085757 restraints weight = 28846.872| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.22 r_work: 0.3450 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11558 Z= 0.131 Angle : 0.682 9.488 15712 Z= 0.343 Chirality : 0.045 0.271 1762 Planarity : 0.005 0.082 1984 Dihedral : 8.719 65.196 1889 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 4.61 % Allowed : 31.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.22), residues: 1423 helix: 0.33 (0.46), residues: 132 sheet: 0.07 (0.25), residues: 479 loop : -1.79 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 54 TYR 0.020 0.001 TYR A 80 PHE 0.009 0.001 PHE J 320 TRP 0.008 0.001 TRP F 272 HIS 0.003 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00294 (11528) covalent geometry : angle 0.67418 (15640) SS BOND : bond 0.00404 ( 18) SS BOND : angle 1.01249 ( 36) hydrogen bonds : bond 0.04152 ( 328) hydrogen bonds : angle 4.80152 ( 885) link_ALPHA1-3 : bond 0.01039 ( 3) link_ALPHA1-3 : angle 1.37067 ( 9) link_ALPHA1-6 : bond 0.00799 ( 3) link_ALPHA1-6 : angle 1.65085 ( 9) link_BETA1-4 : bond 0.00128 ( 6) link_BETA1-4 : angle 2.56636 ( 18) *********************** 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 218 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6183 (tpm170) REVERT: A 87 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7383 (ptp-110) REVERT: B 319 ASP cc_start: 0.7253 (m-30) cc_final: 0.6655 (p0) REVERT: B 341 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 558 LEU cc_start: 0.8417 (tt) cc_final: 0.8069 (tp) REVERT: C 596 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7562 (tpm170) REVERT: D 112 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6816 (tm-30) REVERT: E 65 LYS cc_start: 0.9333 (ttmp) cc_final: 0.9074 (ttmm) REVERT: E 116 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: F 261 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7753 (tpp80) REVERT: F 316 GLN cc_start: 0.8375 (tp40) cc_final: 0.7947 (mm-40) REVERT: G 540 GLU cc_start: 0.8285 (pm20) cc_final: 0.8062 (pm20) REVERT: G 592 PHE cc_start: 0.8621 (t80) cc_final: 0.8375 (t80) REVERT: H 56 LYS cc_start: 0.7999 (mptt) cc_final: 0.7646 (mptt) REVERT: H 59 SER cc_start: 0.9329 (m) cc_final: 0.9052 (t) REVERT: H 78 ASP cc_start: 0.8060 (t0) cc_final: 0.7741 (t70) REVERT: I 83 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7160 (pmm) REVERT: I 89 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: L 56 LYS cc_start: 0.8124 (mppt) cc_final: 0.7594 (mppt) REVERT: L 61 ASN cc_start: 0.8178 (m-40) cc_final: 0.7720 (p0) REVERT: L 115 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8341 (mmtt) outliers start: 55 outliers final: 45 residues processed: 202 average time/residue: 0.5211 time to fit residues: 114.3591 Evaluate side-chains 200 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 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 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 86 LEU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 120 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 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 58 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 595 GLN J 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.105468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084059 restraints weight = 29163.603| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.23 r_work: 0.3419 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11558 Z= 0.169 Angle : 0.716 11.514 15712 Z= 0.360 Chirality : 0.046 0.225 1762 Planarity : 0.005 0.085 1984 Dihedral : 8.672 64.698 1887 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.87 % Favored : 91.99 % Rotamer: Outliers : 4.86 % Allowed : 31.49 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.22), residues: 1423 helix: 0.10 (0.45), residues: 132 sheet: 0.03 (0.25), residues: 479 loop : -1.83 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 136 TYR 0.018 0.001 TYR A 80 PHE 0.013 0.002 PHE I 29 TRP 0.009 0.001 TRP F 272 HIS 0.004 0.001 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00391 (11528) covalent geometry : angle 0.70590 (15640) SS BOND : bond 0.00433 ( 18) SS BOND : angle 1.13495 ( 36) hydrogen bonds : bond 0.04814 ( 328) hydrogen bonds : angle 4.88422 ( 885) link_ALPHA1-3 : bond 0.00928 ( 3) link_ALPHA1-3 : angle 1.94658 ( 9) link_ALPHA1-6 : bond 0.00845 ( 3) link_ALPHA1-6 : angle 1.47743 ( 9) link_BETA1-4 : bond 0.00263 ( 6) link_BETA1-4 : angle 2.89644 ( 18) *********************** 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 217 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6432 (tpm170) REVERT: A 81 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6405 (tp) REVERT: A 87 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7415 (ptp-110) REVERT: B 319 ASP cc_start: 0.7111 (m-30) cc_final: 0.6644 (p0) REVERT: C 558 LEU cc_start: 0.8570 (tt) cc_final: 0.8268 (tp) REVERT: C 596 ARG cc_start: 0.8189 (ttt90) cc_final: 0.7461 (tpm170) REVERT: D 112 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6829 (tm-30) REVERT: E 116 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: F 261 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7901 (tpp80) REVERT: F 316 GLN cc_start: 0.8306 (tp40) cc_final: 0.7959 (mm-40) REVERT: F 339 LYS cc_start: 0.7286 (tppp) cc_final: 0.6780 (tppt) REVERT: G 503 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7795 (m) REVERT: G 540 GLU cc_start: 0.8342 (pm20) cc_final: 0.8099 (pm20) REVERT: G 592 PHE cc_start: 0.8647 (t80) cc_final: 0.8403 (t80) REVERT: H 56 LYS cc_start: 0.8067 (mptt) cc_final: 0.7720 (mppt) REVERT: H 59 SER cc_start: 0.9351 (m) cc_final: 0.9085 (t) REVERT: H 78 ASP cc_start: 0.8090 (t0) cc_final: 0.7777 (t70) REVERT: I 80 TYR cc_start: 0.7828 (m-80) cc_final: 0.7601 (m-80) REVERT: I 83 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7252 (pmm) REVERT: I 89 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: L 56 LYS cc_start: 0.8135 (mppt) cc_final: 0.7566 (mppt) REVERT: L 61 ASN cc_start: 0.8150 (m-40) cc_final: 0.7735 (p0) REVERT: L 115 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8439 (mmtt) outliers start: 58 outliers final: 46 residues processed: 203 average time/residue: 0.4763 time to fit residues: 105.5585 Evaluate side-chains 204 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 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 86 LEU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 120 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 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 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 58 LYS 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 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 23 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.107505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086173 restraints weight = 28974.000| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.23 r_work: 0.3460 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4504 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= 0.129 Angle : 0.692 12.139 15712 Z= 0.347 Chirality : 0.045 0.207 1762 Planarity : 0.005 0.083 1984 Dihedral : 8.133 59.505 1887 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 4.10 % Allowed : 32.24 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.22), residues: 1423 helix: -0.05 (0.44), residues: 138 sheet: 0.04 (0.24), residues: 499 loop : -1.82 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 587 TYR 0.021 0.001 TYR A 80 PHE 0.010 0.001 PHE J 320 TRP 0.010 0.001 TRP F 272 HIS 0.003 0.000 HIS H 139 Details of bonding type rmsd covalent geometry : bond 0.00293 (11528) covalent geometry : angle 0.68567 (15640) SS BOND : bond 0.00359 ( 18) SS BOND : angle 0.96735 ( 36) hydrogen bonds : bond 0.03864 ( 328) hydrogen bonds : angle 4.80592 ( 885) link_ALPHA1-3 : bond 0.01217 ( 3) link_ALPHA1-3 : angle 1.20864 ( 9) link_ALPHA1-6 : bond 0.00923 ( 3) link_ALPHA1-6 : angle 1.60661 ( 9) link_BETA1-4 : bond 0.00176 ( 6) link_BETA1-4 : angle 2.38974 ( 18) ********************** 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 222 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6445 (mmp-170) REVERT: A 38 ARG cc_start: 0.7200 (ptt180) cc_final: 0.6569 (ppt-90) REVERT: A 81 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6410 (tp) REVERT: B 319 ASP cc_start: 0.7152 (m-30) cc_final: 0.6766 (p0) REVERT: B 341 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6651 (mm-30) REVERT: C 506 ASN cc_start: 0.7674 (t0) cc_final: 0.7435 (t0) REVERT: C 558 LEU cc_start: 0.8492 (tt) cc_final: 0.8171 (tp) REVERT: C 596 ARG cc_start: 0.8067 (ttt90) cc_final: 0.7529 (tpm170) REVERT: D 112 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6785 (tm-30) REVERT: E 65 LYS cc_start: 0.9335 (ttmp) cc_final: 0.9073 (ttmm) REVERT: F 261 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7897 (tpp80) REVERT: F 290 ASN cc_start: 0.8594 (m-40) cc_final: 0.8034 (p0) REVERT: F 316 GLN cc_start: 0.8380 (tp40) cc_final: 0.8001 (mm-40) REVERT: F 339 LYS cc_start: 0.7366 (tppp) cc_final: 0.6796 (tppt) REVERT: G 540 GLU cc_start: 0.8269 (pm20) cc_final: 0.8045 (pm20) REVERT: G 592 PHE cc_start: 0.8575 (t80) cc_final: 0.8328 (t80) REVERT: H 56 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7679 (mppt) REVERT: H 59 SER cc_start: 0.9336 (m) cc_final: 0.9072 (t) REVERT: H 78 ASP cc_start: 0.8110 (t0) cc_final: 0.7850 (t0) REVERT: I 89 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: L 56 LYS cc_start: 0.8154 (mppt) cc_final: 0.7625 (mppt) REVERT: L 61 ASN cc_start: 0.8112 (m-40) cc_final: 0.7729 (p0) REVERT: L 115 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8471 (mmtt) outliers start: 49 outliers final: 40 residues processed: 209 average time/residue: 0.5006 time to fit residues: 113.7071 Evaluate side-chains 200 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 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 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 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 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 I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 62 ASP 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 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 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 4 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.102514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081447 restraints weight = 29810.180| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.18 r_work: 0.3367 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11558 Z= 0.291 Angle : 0.842 13.358 15712 Z= 0.426 Chirality : 0.050 0.192 1762 Planarity : 0.006 0.086 1984 Dihedral : 9.104 69.146 1886 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.00 % Favored : 90.86 % Rotamer: Outliers : 4.36 % Allowed : 32.16 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.21), residues: 1423 helix: -0.31 (0.43), residues: 132 sheet: -0.04 (0.24), residues: 501 loop : -2.08 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 587 TYR 0.026 0.003 TYR E 57 PHE 0.024 0.003 PHE I 29 TRP 0.015 0.003 TRP G 597 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00682 (11528) covalent geometry : angle 0.82760 (15640) SS BOND : bond 0.00578 ( 18) SS BOND : angle 1.45448 ( 36) hydrogen bonds : bond 0.06418 ( 328) hydrogen bonds : angle 5.16776 ( 885) link_ALPHA1-3 : bond 0.00541 ( 3) link_ALPHA1-3 : angle 3.10999 ( 9) link_ALPHA1-6 : bond 0.00883 ( 3) link_ALPHA1-6 : angle 1.25900 ( 9) link_BETA1-4 : bond 0.00772 ( 6) link_BETA1-4 : angle 3.62756 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.68 seconds wall clock time: 69 minutes 33.95 seconds (4173.95 seconds total)