Starting phenix.real_space_refine on Sat Oct 12 02:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_38899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_38899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_38899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_38899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3u_38899/10_2024/8y3u_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-5477/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: 7.78, 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: 2.84 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: 1.77 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: 3.97 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3619 1.34 - 1.46: 2946 1.46 - 1.58: 4893 1.58 - 1.70: 1 1.70 - 1.82: 69 Bond restraints: 11528 Sorted by residual: bond pdb=" CB PRO I 41 " pdb=" CG PRO I 41 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.94e+00 bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP D 49 " pdb=" CB ASP D 49 " ideal model delta sigma weight residual 1.524 1.546 -0.021 1.22e-02 6.72e+03 3.06e+00 ... (remaining 11523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 15123 1.73 - 3.47: 395 3.47 - 5.20: 93 5.20 - 6.94: 27 6.94 - 8.67: 2 Bond angle restraints: 15640 Sorted by residual: angle pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" CD PRO I 41 " ideal model delta sigma weight residual 112.00 103.33 8.67 1.40e+00 5.10e-01 3.84e+01 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 113.71 109.48 4.23 9.50e-01 1.11e+00 1.98e+01 angle pdb=" CA ASP H 47 " pdb=" C ASP H 47 " pdb=" N VAL H 48 " ideal model delta sigma weight residual 116.25 120.68 -4.43 1.30e+00 5.92e-01 1.16e+01 angle pdb=" CB LYS E 43 " pdb=" CG LYS E 43 " pdb=" CD LYS E 43 " ideal model delta sigma weight residual 111.30 119.05 -7.75 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA GLN K 595 " pdb=" CB GLN K 595 " pdb=" CG GLN K 595 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 15635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.23: 6311 23.23 - 46.47: 517 46.47 - 69.70: 116 69.70 - 92.93: 28 92.93 - 116.17: 12 Dihedral angle restraints: 6984 sinusoidal: 2874 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS L 108 " pdb=" SG CYS L 108 " pdb=" SG CYS L 135 " pdb=" CB CYS L 135 " ideal model delta sinusoidal sigma weight residual -86.00 -161.12 75.12 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS D 108 " pdb=" SG CYS D 108 " pdb=" SG CYS D 135 " pdb=" CB CYS D 135 " ideal model delta sinusoidal sigma weight residual -86.00 -141.67 55.67 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS H 108 " pdb=" SG CYS H 108 " pdb=" SG CYS H 135 " pdb=" CB CYS H 135 " ideal model delta sinusoidal sigma weight residual -86.00 -136.35 50.35 1 1.00e+01 1.00e-02 3.47e+01 ... (remaining 6981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1400 0.053 - 0.106: 288 0.106 - 0.159: 71 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 1762 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1759 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 40 " 0.093 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO I 41 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO I 41 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 41 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 276 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO J 277 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 277 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 277 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 49 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CG ASP D 49 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP D 49 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP D 49 " 0.011 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 302 2.68 - 3.24: 9554 3.24 - 3.79: 15313 3.79 - 4.35: 20454 4.35 - 4.90: 36480 Nonbonded interactions: 82103 Sorted by model distance: nonbonded pdb=" OG SER I 54 " pdb=" OE2 GLU K 564 " model vdw 2.130 3.040 nonbonded pdb=" N GLU F 318 " pdb=" OE1 GLU F 318 " model vdw 2.194 3.120 nonbonded pdb=" OG SER A 54 " pdb=" OE2 GLU C 564 " model vdw 2.196 3.040 nonbonded pdb=" O SER D 41 " pdb=" OG SER D 41 " model vdw 2.210 3.040 nonbonded pdb=" OG SER E 54 " pdb=" OE2 GLU G 564 " model vdw 2.212 3.040 ... (remaining 82098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = (chain 'D' and resid 32 through 186) selection = (chain 'H' and resid 32 through 186) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 29.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 1.301 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: 1.1411 time to fit residues: 418.2189 Evaluate side-chains 193 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 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 fitting. rotamer outliers: 62 poor density : 179 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 110 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7360 (t0) REVERT: F 316 GLN cc_start: 0.7666 (tp40) cc_final: 0.7367 (mm-40) REVERT: K 527 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7338 (tt) REVERT: L 119 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7993 (p) outliers start: 62 outliers final: 33 residues processed: 229 average time/residue: 1.1290 time to fit residues: 281.8013 Evaluate side-chains 181 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 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 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 527 ILE 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 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS C 560 GLN E 116 GLN J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11528 Z= 0.370 Angle : 0.775 11.861 15640 Z= 0.397 Chirality : 0.048 0.180 1762 Planarity : 0.006 0.084 1984 Dihedral : 11.513 91.290 1892 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.15 % Favored : 91.64 % Rotamer: Outliers : 7.20 % Allowed : 26.63 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1423 helix: 0.29 (0.48), residues: 132 sheet: -0.01 (0.23), residues: 504 loop : -1.99 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 531 HIS 0.005 0.001 HIS D 154 PHE 0.017 0.002 PHE H 153 TYR 0.024 0.002 TYR E 57 ARG 0.007 0.001 ARG J 261 *********************** 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 255 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 169 time to evaluate : 1.251 Fit side-chains REVERT: B 341 GLU cc_start: 0.5638 (mm-30) cc_final: 0.5376 (mm-30) REVERT: C 558 LEU cc_start: 0.8273 (tt) cc_final: 0.7993 (tp) REVERT: D 185 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7786 (pp) REVERT: G 503 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7940 (m) REVERT: G 548 MET cc_start: 0.6320 (ttm) cc_final: 0.6092 (ttm) REVERT: I 65 LYS cc_start: 0.8814 (tppp) cc_final: 0.8208 (tppp) outliers start: 86 outliers final: 52 residues processed: 227 average time/residue: 0.9930 time to fit residues: 247.6289 Evaluate side-chains 197 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 143 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 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 L residue 79 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 125 optimal weight: 0.0020 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 550 ASN C 595 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN L 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3616 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= 0.179 Angle : 0.649 9.161 15640 Z= 0.329 Chirality : 0.044 0.155 1762 Planarity : 0.005 0.075 1984 Dihedral : 10.372 80.285 1892 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 5.19 % Allowed : 29.40 % Favored : 65.41 % 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: -1.23 (0.22), residues: 1423 helix: 0.57 (0.47), residues: 132 sheet: 0.18 (0.23), residues: 504 loop : -1.81 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 104 HIS 0.004 0.001 HIS B 292 PHE 0.009 0.001 PHE J 320 TYR 0.013 0.001 TYR H 99 ARG 0.011 0.001 ARG K 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 237 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 65 LYS cc_start: 0.8757 (tppp) cc_final: 0.8071 (tppp) outliers start: 62 outliers final: 39 residues processed: 221 average time/residue: 1.0638 time to fit residues: 257.3799 Evaluate side-chains 188 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR 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 28 THR 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 J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 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 75 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 550 ASN C 595 GLN J 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3808 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= 0.232 Angle : 0.673 11.577 15640 Z= 0.341 Chirality : 0.045 0.157 1762 Planarity : 0.005 0.073 1984 Dihedral : 10.103 78.174 1890 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 5.19 % Allowed : 30.15 % Favored : 64.66 % 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: -1.26 (0.22), residues: 1423 helix: 0.58 (0.47), residues: 132 sheet: 0.17 (0.23), residues: 504 loop : -1.85 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.002 0.001 HIS I 35 PHE 0.038 0.001 PHE A 68 TYR 0.016 0.001 TYR A 80 ARG 0.010 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 221 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 159 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: C 558 LEU cc_start: 0.8257 (tt) cc_final: 0.7915 (tp) REVERT: I 65 LYS cc_start: 0.8790 (tppp) cc_final: 0.8132 (tppp) outliers start: 62 outliers final: 48 residues processed: 206 average time/residue: 0.9285 time to fit residues: 211.8306 Evaluate side-chains 191 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 247 SER 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 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 142 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 550 ASN C 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11528 Z= 0.207 Angle : 0.657 10.330 15640 Z= 0.333 Chirality : 0.045 0.169 1762 Planarity : 0.005 0.071 1984 Dihedral : 9.590 73.613 1889 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 5.03 % Allowed : 30.49 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.33 (0.22), residues: 1423 helix: 0.52 (0.47), residues: 132 sheet: 0.06 (0.24), residues: 513 loop : -1.86 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 36 HIS 0.003 0.001 HIS H 139 PHE 0.027 0.001 PHE A 68 TYR 0.017 0.001 TYR A 80 ARG 0.011 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 216 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: C 558 LEU cc_start: 0.8241 (tt) cc_final: 0.7918 (tp) outliers start: 60 outliers final: 47 residues processed: 204 average time/residue: 0.9310 time to fit residues: 211.0132 Evaluate side-chains 189 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 583 SER Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 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 J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 550 ASN C 595 GLN J 290 ASN L 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11528 Z= 0.206 Angle : 0.669 9.621 15640 Z= 0.340 Chirality : 0.045 0.179 1762 Planarity : 0.005 0.070 1984 Dihedral : 9.262 70.619 1888 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 4.94 % Allowed : 30.99 % Favored : 64.07 % 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: -1.32 (0.22), residues: 1423 helix: 0.46 (0.46), residues: 132 sheet: 0.06 (0.24), residues: 513 loop : -1.84 (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 H 139 PHE 0.029 0.001 PHE G 592 TYR 0.018 0.001 TYR A 80 ARG 0.012 0.001 ARG A 87 *********************** 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 215 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 156 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: C 558 LEU cc_start: 0.8232 (tt) cc_final: 0.7915 (tp) REVERT: L 56 LYS cc_start: 0.7938 (mppt) cc_final: 0.7626 (mppt) outliers start: 59 outliers final: 51 residues processed: 200 average time/residue: 0.9824 time to fit residues: 216.3307 Evaluate side-chains 194 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 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 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL 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 583 SER Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 142 SER 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 J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 40 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 550 ASN C 595 GLN J 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11528 Z= 0.197 Angle : 0.672 9.151 15640 Z= 0.341 Chirality : 0.045 0.194 1762 Planarity : 0.005 0.069 1984 Dihedral : 8.849 66.587 1888 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.04 % Favored : 93.75 % Rotamer: Outliers : 4.86 % Allowed : 31.99 % Favored : 63.15 % 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: -1.30 (0.22), residues: 1423 helix: 0.36 (0.46), residues: 132 sheet: 0.09 (0.24), residues: 513 loop : -1.81 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 36 HIS 0.006 0.001 HIS C 549 PHE 0.022 0.001 PHE A 68 TYR 0.019 0.001 TYR A 80 ARG 0.012 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 209 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: C 558 LEU cc_start: 0.8272 (tt) cc_final: 0.7949 (tp) REVERT: D 119 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7335 (p) outliers start: 58 outliers final: 49 residues processed: 196 average time/residue: 0.9065 time to fit residues: 197.3757 Evaluate side-chains 191 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 142 SER 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 J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain K residue 586 ASN Chi-restraints excluded: chain K residue 590 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.0060 chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 131 optimal weight: 4.9990 overall best weight: 0.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 307 HIS ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 550 ASN C 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4342 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= 0.212 Angle : 0.685 8.994 15640 Z= 0.347 Chirality : 0.045 0.270 1762 Planarity : 0.005 0.069 1984 Dihedral : 8.590 63.835 1888 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % Rotamer: Outliers : 4.27 % Allowed : 33.00 % Favored : 62.73 % 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: -1.35 (0.22), residues: 1423 helix: 0.04 (0.44), residues: 138 sheet: 0.07 (0.24), residues: 512 loop : -1.82 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.009 0.001 HIS C 549 PHE 0.034 0.001 PHE G 592 TYR 0.018 0.001 TYR A 80 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 fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7591 (ptp-110) cc_final: 0.7242 (mtm110) REVERT: C 558 LEU cc_start: 0.8268 (tt) cc_final: 0.8009 (tp) REVERT: D 117 ASP cc_start: 0.6473 (p0) cc_final: 0.6263 (p0) REVERT: D 119 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7274 (p) outliers start: 51 outliers final: 46 residues processed: 195 average time/residue: 0.8851 time to fit residues: 192.2033 Evaluate side-chains 189 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 142 SER 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 J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS C 550 ASN J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11528 Z= 0.279 Angle : 0.738 12.040 15640 Z= 0.375 Chirality : 0.047 0.240 1762 Planarity : 0.005 0.070 1984 Dihedral : 8.677 63.601 1888 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.45 % Favored : 92.34 % Rotamer: Outliers : 4.36 % Allowed : 32.83 % Favored : 62.81 % 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: -1.40 (0.22), residues: 1423 helix: 0.15 (0.44), residues: 132 sheet: 0.05 (0.24), residues: 507 loop : -1.87 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.008 0.001 HIS C 549 PHE 0.018 0.002 PHE A 68 TYR 0.017 0.002 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 209 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 157 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7315 (mtm110) REVERT: C 558 LEU cc_start: 0.8326 (tt) cc_final: 0.8043 (tp) REVERT: D 117 ASP cc_start: 0.6529 (p0) cc_final: 0.6292 (p0) REVERT: D 119 SER cc_start: 0.7710 (OUTLIER) cc_final: 0.7360 (p) REVERT: G 503 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7987 (m) outliers start: 52 outliers final: 48 residues processed: 199 average time/residue: 0.9109 time to fit residues: 202.9915 Evaluate side-chains 201 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 296 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 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 J residue 276 ILE Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 544 THR Chi-restraints excluded: chain K residue 577 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 overall best weight: 1.4882 ------------------------------------------------------------------------------- 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 550 ASN J 290 ASN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083187 restraints weight = 29414.529| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.24 r_work: 0.3400 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11528 Z= 0.320 Angle : 0.767 12.546 15640 Z= 0.391 Chirality : 0.048 0.195 1762 Planarity : 0.005 0.071 1984 Dihedral : 8.888 65.278 1888 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.78 % Rotamer: Outliers : 4.77 % Allowed : 32.58 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.55 (0.22), residues: 1423 helix: -0.02 (0.44), residues: 132 sheet: 0.05 (0.24), residues: 501 loop : -2.01 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 47 HIS 0.012 0.001 HIS C 549 PHE 0.042 0.002 PHE G 592 TYR 0.019 0.002 TYR E 57 ARG 0.015 0.001 ARG G 587 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.20 seconds wall clock time: 80 minutes 38.75 seconds (4838.75 seconds total)