Starting phenix.real_space_refine on Fri Jan 17 19:31:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3u_38899/01_2025/8y3u_38899.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7113 2.51 5 N 1927 2.21 5 O 2179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11273 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1195 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1195 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.73, per 1000 atoms: 0.69 Number of scatterers: 11273 At special positions: 0 Unit cell: (82.5, 145.2, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2179 8.00 N 1927 7.00 C 7113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 325 " distance=2.04 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 556 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 260 " - pdb=" SG CYS F 325 " distance=2.04 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 135 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 103 " - pdb=" SG CYS I 108 " distance=2.04 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 325 " distance=2.04 Simple disulfide: pdb=" SG CYS K 511 " - pdb=" SG CYS K 556 " distance=2.03 Simple disulfide: pdb=" SG CYS L 108 " - pdb=" SG CYS L 135 " distance=2.03 Simple disulfide: pdb=" SG CYS L 121 " - pdb=" SG CYS L 147 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2606 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 34 sheets defined 11.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.795A pdb=" N GLY A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'C' and resid 557 through 575 removed outlier: 4.037A pdb=" N LEU C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ALA C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 597 removed outlier: 3.856A pdb=" N ARG C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.657A pdb=" N GLY D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 78 through 84 removed outlier: 4.183A pdb=" N THR D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.744A pdb=" N GLY E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.887A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 575 removed outlier: 5.277A pdb=" N GLN G 567 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 removed outlier: 4.435A pdb=" N ARG G 596 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP G 597 " --> pdb=" O LEU G 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 removed outlier: 3.646A pdb=" N GLY H 74 " --> pdb=" O GLU H 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.111A pdb=" N GLY I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'K' and resid 553 through 575 removed outlier: 5.075A pdb=" N GLN K 567 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA K 568 " --> pdb=" O GLU K 564 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA K 575 " --> pdb=" O LEU K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 597 removed outlier: 3.847A pdb=" N ARG K 596 " --> pdb=" O PHE K 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 74 removed outlier: 3.705A pdb=" N GLY L 74 " --> pdb=" O GLU L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 78 through 84 removed outlier: 4.364A pdb=" N THR L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.012A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 50 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.674A pdb=" N PHE A 113 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 244 removed outlier: 3.505A pdb=" N SER B 244 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 259 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 247 through 249 Processing sheet with id=AA6, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'C' and resid 518 through 519 Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.843A pdb=" N HIS D 39 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 36 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 185 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.843A pdb=" N HIS D 39 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 36 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 185 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 160 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'D' and resid 105 through 114 removed outlier: 6.382A pdb=" N GLU D 106 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS D 139 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS D 108 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 141 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN D 110 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLY D 143 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU D 112 " --> pdb=" O GLY D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.967A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.239A pdb=" N CYS E 96 " --> pdb=" O TRP E 114 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP E 114 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG E 98 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 242 through 244 removed outlier: 4.030A pdb=" N SER F 244 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 259 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE F 308 " --> pdb=" O CYS F 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 247 through 249 removed outlier: 6.795A pdb=" N LEU F 248 " --> pdb=" O GLU F 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 282 through 286 removed outlier: 5.245A pdb=" N TRP F 272 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER F 286 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU F 270 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 514 through 515 Processing sheet with id=AC1, first strand: chain 'G' and resid 518 through 519 Processing sheet with id=AC2, first strand: chain 'G' and resid 580 through 581 removed outlier: 3.670A pdb=" N THR G 581 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 98 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 160 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY H 36 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 35 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 580 through 581 removed outlier: 3.670A pdb=" N THR G 581 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 98 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 160 " --> pdb=" O SER H 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AC5, first strand: chain 'H' and resid 109 through 114 Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.643A pdb=" N MET I 34 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 50 " --> pdb=" O TYR I 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.865A pdb=" N ARG I 98 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 241 through 244 removed outlier: 3.680A pdb=" N SER J 244 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR J 259 " --> pdb=" O SER J 244 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 247 through 249 removed outlier: 3.644A pdb=" N THR J 338 " --> pdb=" O TYR J 323 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU J 270 " --> pdb=" O SER J 286 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER J 286 " --> pdb=" O LEU J 270 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TRP J 272 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 514 through 515 Processing sheet with id=AD3, first strand: chain 'K' and resid 518 through 519 Processing sheet with id=AD4, first strand: chain 'L' and resid 42 through 45 removed outlier: 6.990A pdb=" N GLY L 36 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 42 through 45 removed outlier: 6.990A pdb=" N GLY L 36 " --> pdb=" O ILE L 185 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE L 160 " --> pdb=" O SER L 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 86 through 89 Processing sheet with id=AD7, first strand: chain 'L' and resid 105 through 114 removed outlier: 6.237A pdb=" N GLU L 106 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N HIS L 139 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS L 108 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL L 141 " --> pdb=" O CYS L 108 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN L 110 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY L 143 " --> pdb=" O ASN L 110 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU L 112 " --> pdb=" O GLY L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 357 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 3.07 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: 2.500 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.930 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.610 ------------------------------------------------------------------------------- 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 11528 Z= 0.240 Angle : 0.725 8.673 15640 Z= 0.380 Chirality : 0.046 0.265 1762 Planarity : 0.006 0.135 1984 Dihedral : 18.328 116.166 4324 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.48 % Favored : 94.10 % Rotamer: Outliers : 4.19 % Allowed : 27.72 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1423 helix: -0.48 (0.46), residues: 135 sheet: -0.37 (0.24), residues: 464 loop : -1.79 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 36 HIS 0.004 0.001 HIS A 35 PHE 0.010 0.001 PHE C 572 TYR 0.014 0.001 TYR L 99 ARG 0.015 0.001 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6533 (pt) REVERT: D 119 SER cc_start: 0.8313 (t) cc_final: 0.7665 (p) outliers start: 50 outliers final: 26 residues processed: 338 average time/residue: 1.1730 time to fit residues: 429.5757 Evaluate side-chains 193 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 65 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS D 107 ASN D 110 ASN E 116 GLN J 290 ASN K 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.110593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089082 restraints weight = 28993.785| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.25 r_work: 0.3500 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11528 Z= 0.212 Angle : 0.684 10.212 15640 Z= 0.350 Chirality : 0.045 0.179 1762 Planarity : 0.005 0.092 1984 Dihedral : 11.331 92.098 1904 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.69 % Favored : 94.10 % Rotamer: Outliers : 5.19 % Allowed : 28.39 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1423 helix: 0.36 (0.47), residues: 132 sheet: -0.22 (0.23), residues: 512 loop : -1.68 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 597 HIS 0.003 0.001 HIS H 139 PHE 0.012 0.001 PHE G 592 TYR 0.013 0.001 TYR I 80 ARG 0.007 0.001 ARG G 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6549 (mm-30) REVERT: C 547 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8669 (tm) REVERT: D 110 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7614 (t0) REVERT: D 112 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6506 (tm-30) REVERT: E 46 GLU cc_start: 0.7766 (tt0) cc_final: 0.7516 (tt0) REVERT: E 116 GLN cc_start: 0.5328 (OUTLIER) cc_final: 0.5096 (pp30) REVERT: F 316 GLN cc_start: 0.8178 (tp40) cc_final: 0.7763 (mm-40) REVERT: F 339 LYS cc_start: 0.6901 (tppp) cc_final: 0.6577 (tppt) REVERT: H 56 LYS cc_start: 0.8023 (mptt) cc_final: 0.7607 (mptt) REVERT: H 78 ASP cc_start: 0.7534 (t0) cc_final: 0.7319 (t70) REVERT: H 156 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: I 19 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.6093 (ttt90) REVERT: L 119 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8064 (p) outliers start: 62 outliers final: 33 residues processed: 229 average time/residue: 1.1356 time to fit residues: 283.7897 Evaluate side-chains 188 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 0.0020 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 560 GLN D 110 ASN E 116 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.111530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089896 restraints weight = 28725.199| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.30 r_work: 0.3517 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11528 Z= 0.184 Angle : 0.637 10.479 15640 Z= 0.325 Chirality : 0.044 0.185 1762 Planarity : 0.005 0.080 1984 Dihedral : 10.491 85.541 1892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 5.78 % Allowed : 27.81 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1423 helix: 0.51 (0.48), residues: 132 sheet: -0.11 (0.23), residues: 530 loop : -1.60 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 114 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE F 320 TYR 0.014 0.001 TYR A 94 ARG 0.008 0.000 ARG K 587 *********************** 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 235 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7545 (pt) REVERT: C 547 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8592 (tm) REVERT: D 112 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6344 (tm-30) REVERT: E 116 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.5783 (pp30) REVERT: F 261 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7775 (tpp80) REVERT: G 540 GLU cc_start: 0.8028 (pm20) cc_final: 0.7755 (pm20) REVERT: H 56 LYS cc_start: 0.7890 (mptt) cc_final: 0.7521 (mptt) REVERT: H 78 ASP cc_start: 0.7576 (t0) cc_final: 0.7286 (t70) REVERT: I 19 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5988 (ttt-90) REVERT: I 65 LYS cc_start: 0.9356 (tppp) cc_final: 0.8842 (tppp) REVERT: I 83 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7110 (pmm) outliers start: 69 outliers final: 40 residues processed: 215 average time/residue: 1.0364 time to fit residues: 244.4784 Evaluate side-chains 194 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain 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 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 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 116 GLN 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 315 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 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 577 THR Chi-restraints excluded: chain K residue 590 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 6 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.110253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088625 restraints weight = 28698.668| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 4.32 r_work: 0.3491 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11528 Z= 0.198 Angle : 0.642 10.862 15640 Z= 0.323 Chirality : 0.044 0.174 1762 Planarity : 0.005 0.074 1984 Dihedral : 9.872 79.922 1891 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 5.78 % Allowed : 27.81 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1423 helix: 0.53 (0.48), residues: 132 sheet: 0.14 (0.23), residues: 513 loop : -1.64 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 114 HIS 0.004 0.001 HIS B 292 PHE 0.010 0.001 PHE G 592 TYR 0.015 0.001 TYR A 94 ARG 0.009 0.001 ARG G 587 *********************** 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 243 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 174 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7193 (mtm110) REVERT: B 282 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8657 (ttmm) REVERT: B 341 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6503 (mm-30) REVERT: C 596 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7529 (tpm170) REVERT: D 112 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6508 (tm-30) REVERT: D 113 ILE cc_start: 0.8238 (mm) cc_final: 0.7947 (mp) REVERT: G 540 GLU cc_start: 0.8116 (pm20) cc_final: 0.7876 (pm20) REVERT: H 56 LYS cc_start: 0.7928 (mptt) cc_final: 0.7510 (mptt) REVERT: H 59 SER cc_start: 0.9269 (m) cc_final: 0.8953 (t) REVERT: H 78 ASP cc_start: 0.7587 (t0) cc_final: 0.7238 (t70) REVERT: I 65 LYS cc_start: 0.9407 (tppp) cc_final: 0.8929 (tppp) REVERT: I 83 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7153 (pmm) REVERT: I 89 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: L 61 ASN cc_start: 0.8159 (m-40) cc_final: 0.7453 (p0) outliers start: 69 outliers final: 47 residues processed: 226 average time/residue: 1.0580 time to fit residues: 261.7058 Evaluate side-chains 200 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU 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 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 E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 510 LYS 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 141 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.108251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.086680 restraints weight = 28857.982| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.25 r_work: 0.3457 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11528 Z= 0.217 Angle : 0.659 11.588 15640 Z= 0.332 Chirality : 0.045 0.184 1762 Planarity : 0.005 0.072 1984 Dihedral : 9.395 73.888 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.32 % Favored : 93.46 % Rotamer: Outliers : 6.62 % Allowed : 27.14 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1423 helix: 0.33 (0.46), residues: 132 sheet: 0.10 (0.23), residues: 513 loop : -1.66 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 36 HIS 0.002 0.001 HIS I 35 PHE 0.035 0.002 PHE A 68 TYR 0.014 0.001 TYR I 80 ARG 0.011 0.001 ARG G 587 *********************** 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 246 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 167 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7408 (p) REVERT: A 87 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6979 (mtm110) REVERT: B 319 ASP cc_start: 0.7167 (m-30) cc_final: 0.6579 (p0) REVERT: B 341 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6524 (mm-30) REVERT: C 558 LEU cc_start: 0.8377 (tt) cc_final: 0.8105 (tp) REVERT: C 596 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7580 (tpm170) REVERT: D 112 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6478 (tm-30) REVERT: D 113 ILE cc_start: 0.8237 (mm) cc_final: 0.7923 (mp) REVERT: D 156 GLU cc_start: 0.8326 (tt0) cc_final: 0.8100 (tt0) REVERT: G 503 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.7839 (m) REVERT: G 510 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6548 (ptpp) REVERT: G 540 GLU cc_start: 0.8270 (pm20) cc_final: 0.7999 (pm20) REVERT: G 592 PHE cc_start: 0.8575 (t80) cc_final: 0.8372 (t80) REVERT: H 56 LYS cc_start: 0.8013 (mptt) cc_final: 0.7651 (mptt) REVERT: H 59 SER cc_start: 0.9315 (OUTLIER) cc_final: 0.9018 (t) REVERT: H 78 ASP cc_start: 0.7747 (t0) cc_final: 0.7412 (OUTLIER) REVERT: I 19 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6026 (ttt-90) REVERT: I 65 LYS cc_start: 0.9446 (tppp) cc_final: 0.8957 (tppp) REVERT: I 83 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7013 (pmm) REVERT: I 89 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: K 508 GLN cc_start: 0.6755 (mp10) cc_final: 0.6468 (mp10) REVERT: L 61 ASN cc_start: 0.8246 (m-40) cc_final: 0.7640 (p0) outliers start: 79 outliers final: 57 residues processed: 225 average time/residue: 1.0183 time to fit residues: 251.8106 Evaluate side-chains 214 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 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 C residue 588 LYS 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 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 116 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 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 141 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 2.9990 chunk 128 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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 ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.108978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087282 restraints weight = 28920.562| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.25 r_work: 0.3475 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11528 Z= 0.186 Angle : 0.640 10.146 15640 Z= 0.321 Chirality : 0.044 0.200 1762 Planarity : 0.005 0.085 1984 Dihedral : 8.915 69.781 1890 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.11 % Favored : 93.68 % Rotamer: Outliers : 4.69 % Allowed : 29.48 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1423 helix: 0.43 (0.46), residues: 132 sheet: 0.14 (0.23), residues: 513 loop : -1.65 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 36 HIS 0.002 0.001 HIS A 35 PHE 0.023 0.001 PHE A 68 TYR 0.016 0.001 TYR A 94 ARG 0.012 0.001 ARG G 587 *********************** 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 225 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6952 (mtm110) REVERT: B 341 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6457 (mm-30) REVERT: C 558 LEU cc_start: 0.8420 (tt) cc_final: 0.8121 (tp) REVERT: C 596 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7589 (tpm170) REVERT: D 112 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6737 (tm-30) REVERT: D 113 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 63 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9135 (p) REVERT: F 261 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7885 (tpp80) REVERT: G 510 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6750 (ptpp) REVERT: G 540 GLU cc_start: 0.8310 (pm20) cc_final: 0.8056 (pm20) REVERT: G 576 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6796 (t) REVERT: G 592 PHE cc_start: 0.8523 (t80) cc_final: 0.8219 (t80) REVERT: H 56 LYS cc_start: 0.7998 (mptt) cc_final: 0.7664 (mptt) REVERT: H 59 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.9101 (t) REVERT: H 78 ASP cc_start: 0.7865 (t0) cc_final: 0.7555 (OUTLIER) REVERT: I 83 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7024 (pmm) REVERT: I 89 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: J 290 ASN cc_start: 0.8171 (m-40) cc_final: 0.7571 (p0) REVERT: L 61 ASN cc_start: 0.8155 (m-40) cc_final: 0.7656 (p0) REVERT: L 115 LYS cc_start: 0.8267 (mmmt) cc_final: 0.8043 (mmmt) outliers start: 56 outliers final: 40 residues processed: 211 average time/residue: 1.0392 time to fit residues: 241.2281 Evaluate side-chains 196 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 113 ILE 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 63 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 322 THR Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 576 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 62 ASP Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 83 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.0020 chunk 20 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.0614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 508 GLN C 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.111288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.089502 restraints weight = 28834.376| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.30 r_work: 0.3520 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11528 Z= 0.168 Angle : 0.643 9.863 15640 Z= 0.323 Chirality : 0.044 0.222 1762 Planarity : 0.005 0.071 1984 Dihedral : 8.190 64.264 1888 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 3.94 % Allowed : 31.16 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1423 helix: 0.26 (0.44), residues: 138 sheet: 0.28 (0.24), residues: 511 loop : -1.59 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 104 HIS 0.002 0.000 HIS D 139 PHE 0.021 0.001 PHE C 592 TYR 0.018 0.001 TYR A 94 ARG 0.015 0.001 ARG H 54 *********************** 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 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.7070 (mtm110) REVERT: B 341 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6637 (mm-30) REVERT: C 558 LEU cc_start: 0.8394 (tt) cc_final: 0.8106 (tp) REVERT: C 596 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7591 (tpm170) REVERT: D 112 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6676 (tm-30) REVERT: D 113 ILE cc_start: 0.8336 (mm) cc_final: 0.8034 (mp) REVERT: F 261 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7804 (tpp80) REVERT: G 510 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6664 (ptpp) REVERT: G 540 GLU cc_start: 0.8240 (pm20) cc_final: 0.7962 (pm20) REVERT: G 592 PHE cc_start: 0.8463 (t80) cc_final: 0.8166 (t80) REVERT: H 56 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7592 (mptt) REVERT: H 59 SER cc_start: 0.9348 (m) cc_final: 0.9064 (t) REVERT: H 78 ASP cc_start: 0.7818 (t0) cc_final: 0.7498 (OUTLIER) REVERT: I 19 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5908 (ttt-90) REVERT: I 83 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7113 (pmm) REVERT: I 89 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: J 290 ASN cc_start: 0.8131 (m-40) cc_final: 0.7559 (p0) REVERT: L 61 ASN cc_start: 0.8102 (m-40) cc_final: 0.7659 (p0) REVERT: L 115 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8252 (mmtt) outliers start: 47 outliers final: 31 residues processed: 202 average time/residue: 1.1114 time to fit residues: 244.9077 Evaluate side-chains 190 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 510 LYS 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 28 THR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 0.0040 chunk 81 optimal weight: 0.0170 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4630 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.110267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.088553 restraints weight = 28888.722| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.26 r_work: 0.3502 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11528 Z= 0.179 Angle : 0.648 10.128 15640 Z= 0.324 Chirality : 0.044 0.235 1762 Planarity : 0.005 0.069 1984 Dihedral : 7.738 61.230 1883 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.83 % Favored : 94.03 % Rotamer: Outliers : 3.77 % Allowed : 31.83 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1423 helix: 0.15 (0.44), residues: 138 sheet: 0.27 (0.24), residues: 514 loop : -1.61 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 292 PHE 0.018 0.001 PHE A 68 TYR 0.010 0.001 TYR L 99 ARG 0.011 0.001 ARG G 587 *********************** 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 213 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.7069 (mtm110) REVERT: B 319 ASP cc_start: 0.7266 (m-30) cc_final: 0.6818 (p0) REVERT: B 341 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6552 (mm-30) REVERT: C 506 ASN cc_start: 0.8185 (t0) cc_final: 0.7935 (t0) REVERT: C 547 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8724 (tt) REVERT: C 558 LEU cc_start: 0.8421 (tt) cc_final: 0.8138 (tp) REVERT: C 596 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7581 (tpm170) REVERT: D 64 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7950 (mtp85) REVERT: D 112 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6749 (tm-30) REVERT: D 113 ILE cc_start: 0.8391 (mm) cc_final: 0.8057 (mp) REVERT: F 261 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7911 (tpp80) REVERT: F 290 ASN cc_start: 0.8525 (m-40) cc_final: 0.8009 (p0) REVERT: G 503 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8000 (m) REVERT: G 510 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6770 (ptpp) REVERT: G 540 GLU cc_start: 0.8272 (pm20) cc_final: 0.7984 (pm20) REVERT: G 592 PHE cc_start: 0.8512 (t80) cc_final: 0.8225 (t80) REVERT: H 56 LYS cc_start: 0.8124 (mptt) cc_final: 0.7746 (mptt) REVERT: H 59 SER cc_start: 0.9363 (m) cc_final: 0.9087 (t) REVERT: H 78 ASP cc_start: 0.7879 (t0) cc_final: 0.7548 (t70) REVERT: I 83 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7133 (pmm) REVERT: I 89 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: J 290 ASN cc_start: 0.8159 (m-40) cc_final: 0.7581 (p0) REVERT: L 61 ASN cc_start: 0.8108 (m-40) cc_final: 0.7649 (p0) outliers start: 45 outliers final: 32 residues processed: 203 average time/residue: 1.0809 time to fit residues: 239.5263 Evaluate side-chains 192 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 LEU 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 64 ARG Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 89 GLU 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 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 L 39 HIS L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.087011 restraints weight = 29308.395| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.25 r_work: 0.3475 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11528 Z= 0.216 Angle : 0.689 11.735 15640 Z= 0.345 Chirality : 0.045 0.240 1762 Planarity : 0.005 0.069 1984 Dihedral : 7.633 59.687 1881 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 3.85 % Allowed : 31.99 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1423 helix: 0.04 (0.44), residues: 138 sheet: 0.21 (0.24), residues: 514 loop : -1.64 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS L 39 PHE 0.015 0.001 PHE A 68 TYR 0.012 0.001 TYR E 57 ARG 0.011 0.001 ARG G 587 *********************** 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 207 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6498 (tp) REVERT: A 87 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.7092 (mtm110) REVERT: B 319 ASP cc_start: 0.7353 (m-30) cc_final: 0.6894 (p0) REVERT: B 341 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6560 (mm-30) REVERT: C 547 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8790 (tt) REVERT: C 558 LEU cc_start: 0.8444 (tt) cc_final: 0.8161 (tp) REVERT: C 596 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7531 (tpm170) REVERT: D 112 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 113 ILE cc_start: 0.8363 (mm) cc_final: 0.8027 (mp) REVERT: F 261 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7932 (tpp80) REVERT: F 290 ASN cc_start: 0.8517 (m-40) cc_final: 0.7998 (p0) REVERT: G 503 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.7976 (m) REVERT: G 540 GLU cc_start: 0.8297 (pm20) cc_final: 0.8047 (pm20) REVERT: G 592 PHE cc_start: 0.8563 (t80) cc_final: 0.8266 (t80) REVERT: H 56 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7686 (mppt) REVERT: H 59 SER cc_start: 0.9355 (m) cc_final: 0.9085 (t) REVERT: H 78 ASP cc_start: 0.7941 (t0) cc_final: 0.7609 (t70) REVERT: I 83 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7282 (pmm) REVERT: I 89 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: J 290 ASN cc_start: 0.8226 (m-40) cc_final: 0.7607 (p0) REVERT: L 61 ASN cc_start: 0.8061 (m-40) cc_final: 0.7661 (p0) REVERT: L 115 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7644 (mmmt) outliers start: 46 outliers final: 38 residues processed: 195 average time/residue: 1.0696 time to fit residues: 228.5847 Evaluate side-chains 199 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 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 547 LEU 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 97 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 119 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL 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 28 THR 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 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 586 ASN Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 0.7980 chunk 121 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 ** K 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.109549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087839 restraints weight = 28787.148| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.24 r_work: 0.3493 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11528 Z= 0.195 Angle : 0.680 12.533 15640 Z= 0.340 Chirality : 0.045 0.242 1762 Planarity : 0.005 0.068 1984 Dihedral : 7.359 57.052 1881 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 3.43 % Allowed : 32.58 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1423 helix: 0.03 (0.44), residues: 138 sheet: 0.19 (0.24), residues: 516 loop : -1.62 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 597 HIS 0.005 0.001 HIS H 39 PHE 0.015 0.001 PHE A 68 TYR 0.020 0.001 TYR A 80 ARG 0.015 0.001 ARG G 587 ********************** 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 199 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASN cc_start: 0.8487 (m-40) cc_final: 0.7463 (p0) REVERT: B 319 ASP cc_start: 0.7331 (m-30) cc_final: 0.6920 (p0) REVERT: B 341 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6646 (mm-30) REVERT: C 547 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (tt) REVERT: C 558 LEU cc_start: 0.8429 (tt) cc_final: 0.8149 (tp) REVERT: C 596 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7596 (tpm170) REVERT: D 103 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 112 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6887 (tm-30) REVERT: D 113 ILE cc_start: 0.8373 (mm) cc_final: 0.8055 (mp) REVERT: F 261 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7798 (tpp80) REVERT: F 290 ASN cc_start: 0.8475 (m-40) cc_final: 0.8014 (p0) REVERT: G 503 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.7945 (m) REVERT: G 540 GLU cc_start: 0.8267 (pm20) cc_final: 0.8028 (pm20) REVERT: G 592 PHE cc_start: 0.8489 (t80) cc_final: 0.8266 (t80) REVERT: H 55 ASP cc_start: 0.8841 (m-30) cc_final: 0.8387 (p0) REVERT: H 56 LYS cc_start: 0.8143 (mptt) cc_final: 0.7755 (mppt) REVERT: H 59 SER cc_start: 0.9333 (m) cc_final: 0.9060 (t) REVERT: H 78 ASP cc_start: 0.7933 (t0) cc_final: 0.7600 (t70) REVERT: H 150 ASP cc_start: 0.8404 (p0) cc_final: 0.7883 (m-30) REVERT: I 83 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7164 (pmm) REVERT: I 89 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: J 290 ASN cc_start: 0.8208 (m-40) cc_final: 0.7590 (p0) REVERT: L 61 ASN cc_start: 0.8017 (m-40) cc_final: 0.7619 (p0) REVERT: L 115 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7677 (mmmt) outliers start: 41 outliers final: 36 residues processed: 188 average time/residue: 1.0755 time to fit residues: 221.9263 Evaluate side-chains 192 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 547 LEU 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 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 322 THR 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 I residue 28 THR 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 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 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 0.0070 chunk 114 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS ** K 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.109270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.087571 restraints weight = 28804.931| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 4.28 r_work: 0.3484 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11528 Z= 0.198 Angle : 0.688 12.576 15640 Z= 0.343 Chirality : 0.045 0.246 1762 Planarity : 0.005 0.068 1984 Dihedral : 7.111 54.866 1881 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 3.35 % Allowed : 32.91 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1423 helix: 0.02 (0.44), residues: 138 sheet: 0.15 (0.24), residues: 516 loop : -1.62 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS L 39 PHE 0.015 0.001 PHE C 592 TYR 0.018 0.001 TYR A 80 ARG 0.017 0.001 ARG A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8253.02 seconds wall clock time: 148 minutes 57.29 seconds (8937.29 seconds total)