Starting phenix.real_space_refine on Sun Oct 25 18:07:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ztj_74755/10_2026/9ztj_74755.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 87 5.16 5 C 10966 2.51 5 N 2983 2.21 5 O 3430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17466 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3918 Classifications: {'peptide': 490} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.20, per 1000 atoms: 0.24 Number of scatterers: 17466 At special positions: 0 Unit cell: (152.625, 139.425, 147.675, 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 87 16.00 O 3430 8.00 N 2983 7.00 C 10966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 497 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 314 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 490 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 502 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 33 " " NAG A 602 " - " ASN A 309 " " NAG A 603 " - " ASN A 21 " " NAG A 604 " - " ASN A 507 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 298 " " NAG B 603 " - " ASN B 15 " " NAG B 604 " - " ASN B 496 " " NAG C 601 " - " ASN C 33 " " NAG C 602 " - " ASN C 310 " " NAG C 603 " - " ASN C 21 " " NAG C 604 " - " ASN C 508 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 829.4 milliseconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 53 sheets defined 20.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.035A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.725A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 83 through 87 removed outlier: 4.036A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.725A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 83 through 87 removed outlier: 4.035A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.726A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.978A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.126A pdb=" N TRP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.675A pdb=" N MET A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 479 removed outlier: 3.631A pdb=" N GLU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 511 through 522 removed outlier: 3.830A pdb=" N GLU A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.711A pdb=" N ASP B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.767A pdb=" N TRP B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 382 through 400 Processing helix chain 'B' and resid 416 through 469 Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.042A pdb=" N LEU B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.050A pdb=" N ASP C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU C 79 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 394 through 412 Processing helix chain 'C' and resid 428 through 481 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 512 through 524 removed outlier: 3.892A pdb=" N GLU C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLU C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 521 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 522 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.134A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.971A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.559A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA7, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.135A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.972A pdb=" N LEU I 33 " --> pdb=" O HIS I 49 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.560A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AB3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.134A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.973A pdb=" N LEU K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.559A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AB8, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AC1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.056A pdb=" N LEU A 51 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N CYS A 297 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.889A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 89 " --> pdb=" O MET A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.424A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU A 189 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 266 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 271 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS A 120 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS A 282 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 118 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.424A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU A 189 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.585A pdb=" N CYS A 146 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AC8, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AC9, first strand: chain 'A' and resid 483 through 485 Processing sheet with id=AD1, first strand: chain 'B' and resid 6 through 11 removed outlier: 3.624A pdb=" N CYS B 8 " --> pdb=" O HIS B 367 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 365 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.362A pdb=" N GLU B 18 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AD4, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AD5, first strand: chain 'B' and resid 45 through 48 removed outlier: 7.055A pdb=" N LEU B 45 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N CYS B 286 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.770A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 83 " --> pdb=" O MET B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.411A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 179 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 264 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 269 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS B 114 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS B 271 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 112 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.411A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 179 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AE1, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.778A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AE3, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AE4, first strand: chain 'B' and resid 472 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.719A pdb=" N GLN C 12 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 377 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AE8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.057A pdb=" N LEU C 51 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N CYS C 298 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.827A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 89 " --> pdb=" O MET C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.489A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU C 189 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C 266 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 271 " --> pdb=" O HIS C 120 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS C 120 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS C 283 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 118 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.489A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 189 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AF5, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.631A pdb=" N ALA C 145 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ALA C 152 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AF7, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AF8, first strand: chain 'C' and resid 484 through 486 659 hydrogen bonds defined for protein. 1698 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: 3.44 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.41: 7497 1.41 - 1.71: 10245 1.71 - 2.02: 127 2.02 - 2.33: 0 2.33 - 2.63: 1 Bond restraints: 17870 Sorted by residual: bond pdb=" C5 NAG A 604 " pdb=" C6 NAG A 604 " ideal model delta sigma weight residual 1.513 2.631 -1.118 2.00e-02 2.50e+03 3.12e+03 bond pdb=" C6 NAG A 604 " pdb=" O6 NAG A 604 " ideal model delta sigma weight residual 1.408 1.751 -0.343 2.00e-02 2.50e+03 2.95e+02 bond pdb=" C GLU A 503 " pdb=" O GLU A 503 " ideal model delta sigma weight residual 1.236 1.103 0.134 1.15e-02 7.56e+03 1.35e+02 bond pdb=" C ARG C 82 " pdb=" N VAL C 83 " ideal model delta sigma weight residual 1.329 1.289 0.040 7.30e-03 1.88e+04 3.02e+01 bond pdb=" C ARG A 82 " pdb=" N VAL A 83 " ideal model delta sigma weight residual 1.329 1.292 0.037 7.30e-03 1.88e+04 2.52e+01 ... (remaining 17865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 24121 5.00 - 10.01: 98 10.01 - 15.01: 8 15.01 - 20.01: 5 20.01 - 25.02: 1 Bond angle restraints: 24233 Sorted by residual: angle pdb=" C GLU A 503 " pdb=" CA GLU A 503 " pdb=" CB GLU A 503 " ideal model delta sigma weight residual 110.88 126.97 -16.09 1.57e+00 4.06e-01 1.05e+02 angle pdb=" C MET A 502 " pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 120.44 108.68 11.76 1.30e+00 5.92e-01 8.18e+01 angle pdb=" C ARG A 82 " pdb=" CA ARG A 82 " pdb=" CB ARG A 82 " ideal model delta sigma weight residual 109.35 126.45 -17.10 1.98e+00 2.55e-01 7.45e+01 angle pdb=" C ARG C 82 " pdb=" CA ARG C 82 " pdb=" CB ARG C 82 " ideal model delta sigma weight residual 109.35 126.27 -16.92 1.98e+00 2.55e-01 7.30e+01 angle pdb=" CA GLU A 503 " pdb=" C GLU A 503 " pdb=" N SER A 504 " ideal model delta sigma weight residual 117.07 126.78 -9.71 1.14e+00 7.69e-01 7.25e+01 ... (remaining 24228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9622 17.94 - 35.87: 1094 35.87 - 53.81: 295 53.81 - 71.75: 51 71.75 - 89.68: 27 Dihedral angle restraints: 11089 sinusoidal: 4885 harmonic: 6204 Sorted by residual: dihedral pdb=" CB CYS C 498 " pdb=" SG CYS C 498 " pdb=" SG CYS C 502 " pdb=" CB CYS C 502 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS A 497 " pdb=" SG CYS A 497 " pdb=" SG CYS A 501 " pdb=" CB CYS A 501 " ideal model delta sinusoidal sigma weight residual 93.00 161.11 -68.11 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 490 " pdb=" CB CYS B 490 " ideal model delta sinusoidal sigma weight residual 93.00 147.27 -54.27 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 11086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2475 0.100 - 0.200: 194 0.200 - 0.299: 11 0.299 - 0.399: 5 0.399 - 0.499: 4 Chirality restraints: 2689 Sorted by residual: chirality pdb=" C2 SIA J 7 " pdb=" O3 GAL J 6 " pdb=" C1 SIA J 7 " pdb=" O6 SIA J 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.80e+02 chirality pdb=" C2 SIA F 7 " pdb=" O3 GAL F 6 " pdb=" C1 SIA F 7 " pdb=" O6 SIA F 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.66e+02 chirality pdb=" C2 SIA E 7 " pdb=" O3 GAL E 6 " pdb=" C1 SIA E 7 " pdb=" O6 SIA E 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.59e+02 ... (remaining 2686 not shown) Planarity restraints: 3111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 603 " -0.339 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C7 NAG C 603 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 603 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C 603 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 603 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.307 2.00e-02 2.50e+03 2.61e-01 8.54e+02 pdb=" C7 NAG A 604 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.457 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 604 " 0.289 2.00e-02 2.50e+03 2.42e-01 7.33e+02 pdb=" C7 NAG B 604 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG B 604 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 604 " -0.410 2.00e-02 2.50e+03 pdb=" O7 NAG B 604 " 0.010 2.00e-02 2.50e+03 ... (remaining 3108 not shown) Histogram of nonbonded interaction distances: 0.80 - 1.62: 18 1.62 - 2.44: 26 2.44 - 3.26: 16449 3.26 - 4.08: 44991 4.08 - 4.90: 82108 Warning: very small nonbonded interaction distances. Nonbonded interactions: 143592 Sorted by model distance: nonbonded pdb=" CB VAL D 2 " pdb=" OG SER D 25 " model vdw 0.798 3.470 nonbonded pdb=" CB VAL G 2 " pdb=" OG SER G 25 " model vdw 0.798 3.470 nonbonded pdb=" CB VAL H 2 " pdb=" OG SER H 25 " model vdw 0.798 3.470 nonbonded pdb=" CG2 VAL H 2 " pdb=" CB SER H 25 " model vdw 0.805 3.860 nonbonded pdb=" CG2 VAL D 2 " pdb=" CB SER D 25 " model vdw 0.805 3.860 ... (remaining 143587 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 'B' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 487 or resid 489 through 604)) selection = (chain 'C' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 499 or resid 501 through 604)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.790 Find NCS groups from input model: 0.340 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 : 0.011 1.118 17922 Z= 0.640 Angle : 0.987 25.017 24365 Z= 0.549 Chirality : 0.057 0.499 2689 Planarity : 0.013 0.293 3099 Dihedral : 16.268 89.683 7058 Min Nonbonded Distance : 0.798 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 2.52 % Allowed : 20.59 % Favored : 76.89 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2121 helix: 1.30 (0.27), residues: 353 sheet: -0.53 (0.25), residues: 471 loop : -1.52 (0.15), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG H 30 TYR 0.029 0.002 TYR A 472 PHE 0.015 0.002 PHE C 363 TRP 0.015 0.001 TRP D 99 HIS 0.013 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00999 / 0.51 (17870) covalent geometry : angle 0.96102 / 0.54 (24233) SS BOND : bond 0.00469 / 0.25 ( 21) SS BOND : angle 1.35676 / 0.78 ( 42) hydrogen bonds : bond 0.18508 / 12.38 ( 620) hydrogen bonds : angle 7.96304 / 5.48 ( 1698) Misc. bond : bond 0.51092 / 26.89 ( 1) link_ALPHA1-3 : bond 0.00923 / 0.44 ( 3) link_ALPHA1-3 : angle 1.12849 / 0.61 ( 9) link_BETA1-2 : bond 0.00167 / 0.09 ( 3) link_BETA1-2 : angle 0.83899 / 0.46 ( 9) link_BETA1-4 : bond 0.00424 / 0.25 ( 9) link_BETA1-4 : angle 2.80369 / 1.67 ( 27) link_BETA2-3 : bond 0.00136 / 0.07 ( 3) link_BETA2-3 : angle 6.40220 / 3.29 ( 9) link_NAG-ASN : bond 0.00863 / 0.45 ( 12) link_NAG-ASN : angle 4.33061 / 2.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 72 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.5957 (m-30) REVERT: G 64 ARG cc_start: 0.7475 (ttm110) cc_final: 0.7118 (ttp-110) REVERT: G 72 ASP cc_start: 0.5789 (OUTLIER) cc_final: 0.5561 (m-30) REVERT: A 31 GLU cc_start: 0.7391 (tt0) cc_final: 0.6773 (pt0) REVERT: A 64 ASP cc_start: 0.6532 (t0) cc_final: 0.6329 (t0) REVERT: A 117 ARG cc_start: 0.6679 (mmm160) cc_final: 0.6417 (mmm160) REVERT: A 196 ASN cc_start: 0.7283 (m-40) cc_final: 0.6856 (m110) REVERT: A 241 ASP cc_start: 0.5665 (m-30) cc_final: 0.5401 (m-30) REVERT: A 248 LYS cc_start: 0.6950 (mmtt) cc_final: 0.6750 (mmtp) REVERT: A 282 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7723 (mtpp) REVERT: A 289 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7988 (mmtt) REVERT: A 312 MET cc_start: 0.7651 (mmt) cc_final: 0.7289 (mtt) REVERT: A 330 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8251 (mttt) REVERT: A 374 TRP cc_start: 0.8199 (m-10) cc_final: 0.7978 (m-10) REVERT: A 377 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: A 422 GLU cc_start: 0.6710 (mp0) cc_final: 0.6257 (mp0) REVERT: A 428 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.5777 (mmp-170) REVERT: A 430 ILE cc_start: 0.7700 (mt) cc_final: 0.7443 (mp) REVERT: A 472 TYR cc_start: 0.7477 (t80) cc_final: 0.7152 (t80) REVERT: B 24 MET cc_start: 0.8191 (mmt) cc_final: 0.7959 (mmt) REVERT: B 25 GLU cc_start: 0.7603 (tt0) cc_final: 0.7004 (pt0) REVERT: B 70 MET cc_start: 0.7703 (mmm) cc_final: 0.7492 (mmm) REVERT: B 108 MET cc_start: 0.7111 (ttp) cc_final: 0.6886 (ttp) REVERT: B 186 ASN cc_start: 0.7070 (m-40) cc_final: 0.6676 (m110) REVERT: B 230 MET cc_start: 0.7341 (mtp) cc_final: 0.7026 (mtt) REVERT: B 231 ASP cc_start: 0.5572 (m-30) cc_final: 0.5295 (m-30) REVERT: B 258 ASN cc_start: 0.8392 (m110) cc_final: 0.8139 (m-40) REVERT: B 271 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7728 (mtpp) REVERT: B 401 MET cc_start: 0.7060 (mmt) cc_final: 0.6802 (mmt) REVERT: B 417 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.5900 (mmp-170) REVERT: B 419 ILE cc_start: 0.7754 (mm) cc_final: 0.7512 (mm) REVERT: B 465 ARG cc_start: 0.6883 (tmm-80) cc_final: 0.6673 (ttp80) REVERT: C 31 GLU cc_start: 0.7398 (tt0) cc_final: 0.6766 (pt0) REVERT: C 98 ASP cc_start: 0.7006 (t0) cc_final: 0.6760 (t0) REVERT: C 99 LEU cc_start: 0.7009 (mt) cc_final: 0.6644 (mt) REVERT: C 117 ARG cc_start: 0.6795 (mmm160) cc_final: 0.6450 (mmm160) REVERT: C 140 LEU cc_start: 0.8114 (mt) cc_final: 0.7811 (mt) REVERT: C 248 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6835 (mmtp) REVERT: C 283 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7749 (mtpp) REVERT: C 294 GLU cc_start: 0.6738 (pm20) cc_final: 0.6401 (pm20) REVERT: C 301 LYS cc_start: 0.7548 (mtmm) cc_final: 0.6986 (mttp) REVERT: C 313 MET cc_start: 0.7365 (mmt) cc_final: 0.7047 (mtt) REVERT: C 325 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6802 (mt-10) REVERT: C 375 TRP cc_start: 0.8277 (m-10) cc_final: 0.7689 (m-10) REVERT: C 426 ASN cc_start: 0.7849 (t0) cc_final: 0.7594 (t0) REVERT: C 429 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.5957 (mmp-170) REVERT: C 494 PHE cc_start: 0.8393 (m-80) cc_final: 0.8094 (m-80) REVERT: C 503 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6648 (mmt) outliers start: 47 outliers final: 24 residues processed: 355 average time/residue: 0.1480 time to fit residues: 76.6411 Evaluate side-chains 270 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 HIS A 38 HIS A 478 GLN C 47 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109129 restraints weight = 19761.464| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.79 r_work: 0.3089 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17922 Z= 0.212 Angle : 0.682 8.440 24365 Z= 0.344 Chirality : 0.048 0.317 2689 Planarity : 0.005 0.047 3099 Dihedral : 8.283 85.741 3082 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 4.29 % Allowed : 19.20 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2121 helix: 1.66 (0.27), residues: 367 sheet: -0.36 (0.26), residues: 477 loop : -1.34 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 64 TYR 0.014 0.002 TYR B 499 PHE 0.020 0.002 PHE H 100A TRP 0.016 0.002 TRP H 35A HIS 0.007 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (17870) covalent geometry : angle 0.65300 / 0.34 (24233) SS BOND : bond 0.00391 / 0.26 ( 21) SS BOND : angle 0.84033 / 0.49 ( 42) hydrogen bonds : bond 0.04352 / 3.02 ( 620) hydrogen bonds : angle 5.62041 / 3.90 ( 1698) Misc. bond : bond 0.00829 / 0.44 ( 1) link_ALPHA1-3 : bond 0.00914 / 0.44 ( 3) link_ALPHA1-3 : angle 1.31554 / 0.70 ( 9) link_BETA1-2 : bond 0.00219 / 0.11 ( 3) link_BETA1-2 : angle 0.84561 / 0.45 ( 9) link_BETA1-4 : bond 0.00333 / 0.16 ( 9) link_BETA1-4 : angle 2.89365 / 1.73 ( 27) link_BETA2-3 : bond 0.00818 / 0.38 ( 3) link_BETA2-3 : angle 5.88242 / 3.13 ( 9) link_NAG-ASN : bond 0.00608 / 0.31 ( 12) link_NAG-ASN : angle 3.34267 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 SER cc_start: 0.8322 (p) cc_final: 0.8080 (m) REVERT: I 68 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: G 64 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7863 (ttp-170) REVERT: K 10 SER cc_start: 0.8744 (t) cc_final: 0.8406 (p) REVERT: K 68 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: A 31 GLU cc_start: 0.7792 (tt0) cc_final: 0.7258 (pt0) REVERT: A 117 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7907 (mmm160) REVERT: A 311 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 374 TRP cc_start: 0.8550 (m-10) cc_final: 0.8269 (m-10) REVERT: A 377 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: A 422 GLU cc_start: 0.7819 (mp0) cc_final: 0.7383 (mp0) REVERT: A 428 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7532 (mmp-170) REVERT: B 25 GLU cc_start: 0.7938 (tt0) cc_final: 0.7468 (pt0) REVERT: B 70 MET cc_start: 0.8756 (mmm) cc_final: 0.8511 (mmm) REVERT: B 258 ASN cc_start: 0.9260 (m110) cc_final: 0.8945 (m110) REVERT: B 301 MET cc_start: 0.8192 (mtt) cc_final: 0.7944 (mtt) REVERT: B 398 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6927 (mt) REVERT: B 417 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7612 (mmp-170) REVERT: B 419 ILE cc_start: 0.8809 (mm) cc_final: 0.8531 (mm) REVERT: B 465 ARG cc_start: 0.7336 (tmm-80) cc_final: 0.7092 (ttp80) REVERT: C 31 GLU cc_start: 0.7861 (tt0) cc_final: 0.7338 (pt0) REVERT: C 64 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6564 (t0) REVERT: C 98 ASP cc_start: 0.7522 (t0) cc_final: 0.7314 (t0) REVERT: C 248 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8206 (mmtp) REVERT: C 294 GLU cc_start: 0.7309 (pm20) cc_final: 0.7004 (pm20) REVERT: C 301 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7666 (mttp) REVERT: C 429 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7580 (mmp-170) REVERT: C 503 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5598 (mpt) outliers start: 80 outliers final: 42 residues processed: 292 average time/residue: 0.1577 time to fit residues: 66.3192 Evaluate side-chains 252 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [140, 29, 200, 91, 72, 35, 144, 70, 180, 64, 161] chunk 140 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 200 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 53 ASN I 53 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN B 186 ASN C 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110524 restraints weight = 19930.245| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.79 r_work: 0.3057 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17922 Z= 0.132 Angle : 0.581 7.531 24365 Z= 0.293 Chirality : 0.045 0.299 2689 Planarity : 0.004 0.038 3099 Dihedral : 7.848 81.956 3063 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 3.97 % Allowed : 19.03 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2121 helix: 1.98 (0.27), residues: 369 sheet: -0.14 (0.26), residues: 468 loop : -1.23 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.012 0.001 TYR C 295 PHE 0.010 0.001 PHE B 351 TRP 0.014 0.001 TRP G 99 HIS 0.003 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (17870) covalent geometry : angle 0.55470 / 0.29 (24233) SS BOND : bond 0.00196 / 0.13 ( 21) SS BOND : angle 0.66249 / 0.38 ( 42) hydrogen bonds : bond 0.03821 / 2.61 ( 620) hydrogen bonds : angle 5.18025 / 3.61 ( 1698) Misc. bond : bond 0.00185 / 0.10 ( 1) link_ALPHA1-3 : bond 0.00795 / 0.38 ( 3) link_ALPHA1-3 : angle 1.26922 / 0.69 ( 9) link_BETA1-2 : bond 0.00246 / 0.12 ( 3) link_BETA1-2 : angle 0.82170 / 0.44 ( 9) link_BETA1-4 : bond 0.00364 / 0.22 ( 9) link_BETA1-4 : angle 2.63820 / 1.60 ( 27) link_BETA2-3 : bond 0.00764 / 0.35 ( 3) link_BETA2-3 : angle 5.26291 / 2.81 ( 9) link_NAG-ASN : bond 0.00680 / 0.35 ( 12) link_NAG-ASN : angle 2.84770 / 1.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 64 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7868 (ttp-170) REVERT: H 70 SER cc_start: 0.8253 (p) cc_final: 0.7925 (m) REVERT: D 70 SER cc_start: 0.8324 (p) cc_final: 0.8061 (m) REVERT: I 61 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7955 (ptt90) REVERT: I 68 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: G 70 SER cc_start: 0.8280 (p) cc_final: 0.7988 (m) REVERT: K 68 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: A 117 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7756 (mmm160) REVERT: A 186 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 240 MET cc_start: 0.9163 (mtt) cc_final: 0.8722 (mtt) REVERT: A 311 SER cc_start: 0.8349 (p) cc_final: 0.7917 (t) REVERT: A 374 TRP cc_start: 0.8588 (m-10) cc_final: 0.8314 (m-10) REVERT: A 428 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7376 (mmp-170) REVERT: B 25 GLU cc_start: 0.7910 (tt0) cc_final: 0.7379 (pt0) REVERT: B 70 MET cc_start: 0.8664 (mmm) cc_final: 0.8454 (mmm) REVERT: B 258 ASN cc_start: 0.9217 (m110) cc_final: 0.8993 (m-40) REVERT: B 301 MET cc_start: 0.8184 (mtt) cc_final: 0.7888 (mtt) REVERT: B 398 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6857 (mt) REVERT: B 417 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7406 (mmp-170) REVERT: B 419 ILE cc_start: 0.8695 (mm) cc_final: 0.8411 (mm) REVERT: B 465 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7181 (ttp80) REVERT: B 504 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: C 31 GLU cc_start: 0.7811 (tt0) cc_final: 0.7253 (pt0) REVERT: C 98 ASP cc_start: 0.7395 (t0) cc_final: 0.7174 (t0) REVERT: C 248 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8149 (mmtp) REVERT: C 301 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7618 (mttp) REVERT: C 429 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7457 (mmp-170) REVERT: C 503 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5559 (mpt) outliers start: 74 outliers final: 43 residues processed: 279 average time/residue: 0.1507 time to fit residues: 61.6142 Evaluate side-chains 255 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [84, 139, 1, 182, 25, 163, 66, 38, 20, 101, 68] chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 101 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN B 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109216 restraints weight = 19927.110| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.78 r_work: 0.3036 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17922 Z= 0.123 Angle : 0.563 8.032 24365 Z= 0.284 Chirality : 0.045 0.291 2689 Planarity : 0.004 0.035 3099 Dihedral : 7.616 81.677 3061 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 3.91 % Allowed : 18.93 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2121 helix: 2.20 (0.27), residues: 368 sheet: -0.06 (0.26), residues: 468 loop : -1.13 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.011 0.001 TYR C 473 PHE 0.010 0.001 PHE H 100A TRP 0.012 0.001 TRP G 99 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17870) covalent geometry : angle 0.53697 / 0.28 (24233) SS BOND : bond 0.00190 / 0.12 ( 21) SS BOND : angle 0.59567 / 0.33 ( 42) hydrogen bonds : bond 0.03590 / 2.43 ( 620) hydrogen bonds : angle 4.95791 / 3.46 ( 1698) Misc. bond : bond 0.00379 / 0.20 ( 1) link_ALPHA1-3 : bond 0.00767 / 0.36 ( 3) link_ALPHA1-3 : angle 1.23835 / 0.67 ( 9) link_BETA1-2 : bond 0.00302 / 0.15 ( 3) link_BETA1-2 : angle 0.77898 / 0.41 ( 9) link_BETA1-4 : bond 0.00377 / 0.22 ( 9) link_BETA1-4 : angle 2.61747 / 1.59 ( 27) link_BETA2-3 : bond 0.00664 / 0.31 ( 3) link_BETA2-3 : angle 5.19372 / 2.78 ( 9) link_NAG-ASN : bond 0.00661 / 0.33 ( 12) link_NAG-ASN : angle 2.73624 / 1.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 64 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7796 (ttp-170) REVERT: H 70 SER cc_start: 0.8275 (p) cc_final: 0.7913 (m) REVERT: D 70 SER cc_start: 0.8293 (p) cc_final: 0.8028 (m) REVERT: I 68 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: G 70 SER cc_start: 0.8253 (p) cc_final: 0.7950 (m) REVERT: K 68 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: A 117 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7668 (mmm160) REVERT: A 186 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 311 SER cc_start: 0.8366 (p) cc_final: 0.7949 (t) REVERT: A 374 TRP cc_start: 0.8653 (m-10) cc_final: 0.8341 (m-10) REVERT: A 428 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7345 (mmp-170) REVERT: B 25 GLU cc_start: 0.7921 (tt0) cc_final: 0.7297 (pt0) REVERT: B 70 MET cc_start: 0.8633 (mmm) cc_final: 0.8426 (mmm) REVERT: B 258 ASN cc_start: 0.9234 (m110) cc_final: 0.9019 (m-40) REVERT: B 301 MET cc_start: 0.8157 (mtt) cc_final: 0.7866 (mtt) REVERT: B 398 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6772 (mt) REVERT: B 417 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7315 (mmp-170) REVERT: B 419 ILE cc_start: 0.8630 (mm) cc_final: 0.8334 (mm) REVERT: B 465 ARG cc_start: 0.7523 (tmm-80) cc_final: 0.7152 (ttp80) REVERT: B 504 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: C 31 GLU cc_start: 0.7750 (tt0) cc_final: 0.7125 (pt0) REVERT: C 98 ASP cc_start: 0.7413 (t0) cc_final: 0.7207 (t0) REVERT: C 174 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8178 (mt) REVERT: C 248 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8138 (mmtp) REVERT: C 301 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7543 (mttp) REVERT: C 375 TRP cc_start: 0.8693 (m-10) cc_final: 0.8132 (m-10) REVERT: C 429 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7378 (mmp-170) REVERT: C 503 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.5497 (mpt) outliers start: 73 outliers final: 54 residues processed: 268 average time/residue: 0.1479 time to fit residues: 58.3487 Evaluate side-chains 265 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [69, 42, 143, 17, 94, 181, 35, 188, 70, 199, 204] chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 188 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104213 restraints weight = 19965.411| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.79 r_work: 0.2969 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17922 Z= 0.252 Angle : 0.670 9.576 24365 Z= 0.336 Chirality : 0.049 0.363 2689 Planarity : 0.004 0.051 3099 Dihedral : 8.113 89.964 3059 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 4.66 % Allowed : 19.36 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2121 helix: 1.76 (0.27), residues: 383 sheet: -0.34 (0.25), residues: 523 loop : -1.21 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.012 0.002 TYR C 295 PHE 0.023 0.002 PHE H 100A TRP 0.021 0.002 TRP B 80 HIS 0.008 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.25 (17870) covalent geometry : angle 0.63921 / 0.33 (24233) SS BOND : bond 0.00368 / 0.22 ( 21) SS BOND : angle 0.88723 / 0.49 ( 42) hydrogen bonds : bond 0.04209 / 2.79 ( 620) hydrogen bonds : angle 5.19424 / 3.62 ( 1698) Misc. bond : bond 0.00377 / 0.20 ( 1) link_ALPHA1-3 : bond 0.00789 / 0.37 ( 3) link_ALPHA1-3 : angle 1.28354 / 0.68 ( 9) link_BETA1-2 : bond 0.00416 / 0.19 ( 3) link_BETA1-2 : angle 0.95530 / 0.48 ( 9) link_BETA1-4 : bond 0.00386 / 0.20 ( 9) link_BETA1-4 : angle 2.94699 / 1.79 ( 27) link_BETA2-3 : bond 0.00841 / 0.39 ( 3) link_BETA2-3 : angle 6.90398 / 3.64 ( 9) link_NAG-ASN : bond 0.00574 / 0.28 ( 12) link_NAG-ASN : angle 2.97258 / 1.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 205 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8465 (p) cc_final: 0.8069 (m) REVERT: D 70 SER cc_start: 0.8396 (p) cc_final: 0.8103 (m) REVERT: I 68 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: G 70 SER cc_start: 0.8333 (p) cc_final: 0.7986 (m) REVERT: K 68 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: A 117 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7846 (mmm160) REVERT: A 146 CYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7948 (m) REVERT: A 186 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 311 SER cc_start: 0.8369 (p) cc_final: 0.7955 (t) REVERT: A 334 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (mp) REVERT: A 374 TRP cc_start: 0.8846 (m-10) cc_final: 0.8516 (m-10) REVERT: A 428 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7460 (mmp-170) REVERT: B 25 GLU cc_start: 0.7953 (tt0) cc_final: 0.7298 (pt0) REVERT: B 109 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 301 MET cc_start: 0.8213 (mtt) cc_final: 0.7938 (mtt) REVERT: B 417 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7673 (mmt-90) REVERT: B 465 ARG cc_start: 0.7773 (tmm-80) cc_final: 0.7412 (ttp80) REVERT: B 504 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5321 (m-80) REVERT: C 31 GLU cc_start: 0.7678 (tt0) cc_final: 0.7102 (pt0) REVERT: C 248 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8190 (mmtp) REVERT: C 301 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7720 (mttp) REVERT: C 429 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7427 (mmp-170) REVERT: C 439 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: C 503 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5471 (mpt) outliers start: 87 outliers final: 60 residues processed: 274 average time/residue: 0.1492 time to fit residues: 60.0147 Evaluate side-chains 263 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [111, 89, 124, 127, 179, 154, 66, 195, 54, 56, 83] chunk 111 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105379 restraints weight = 19917.012| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.77 r_work: 0.3019 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17922 Z= 0.164 Angle : 0.597 8.378 24365 Z= 0.299 Chirality : 0.046 0.346 2689 Planarity : 0.004 0.037 3099 Dihedral : 7.981 87.513 3058 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 4.29 % Allowed : 19.46 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2121 helix: 1.91 (0.28), residues: 383 sheet: -0.26 (0.25), residues: 512 loop : -1.15 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.011 0.001 TYR G 59 PHE 0.014 0.001 PHE H 100A TRP 0.014 0.001 TRP G 99 HIS 0.005 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (17870) covalent geometry : angle 0.56619 / 0.29 (24233) SS BOND : bond 0.00265 / 0.17 ( 21) SS BOND : angle 0.73142 / 0.41 ( 42) hydrogen bonds : bond 0.03768 / 2.50 ( 620) hydrogen bonds : angle 5.01883 / 3.50 ( 1698) Misc. bond : bond 0.00363 / 0.19 ( 1) link_ALPHA1-3 : bond 0.00759 / 0.36 ( 3) link_ALPHA1-3 : angle 1.25680 / 0.68 ( 9) link_BETA1-2 : bond 0.00331 / 0.16 ( 3) link_BETA1-2 : angle 0.83557 / 0.42 ( 9) link_BETA1-4 : bond 0.00398 / 0.23 ( 9) link_BETA1-4 : angle 2.69659 / 1.66 ( 27) link_BETA2-3 : bond 0.00632 / 0.29 ( 3) link_BETA2-3 : angle 5.94721 / 3.17 ( 9) link_NAG-ASN : bond 0.00633 / 0.34 ( 12) link_NAG-ASN : angle 3.13552 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 212 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8455 (p) cc_final: 0.8069 (m) REVERT: D 70 SER cc_start: 0.8398 (p) cc_final: 0.8105 (m) REVERT: I 68 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: G 70 SER cc_start: 0.8373 (p) cc_final: 0.8001 (m) REVERT: K 68 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: A 117 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7779 (mmm160) REVERT: A 146 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7981 (m) REVERT: A 186 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (mp) REVERT: A 311 SER cc_start: 0.8348 (p) cc_final: 0.7953 (t) REVERT: A 374 TRP cc_start: 0.8868 (m-10) cc_final: 0.8542 (m-10) REVERT: A 428 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7439 (mmp-170) REVERT: B 25 GLU cc_start: 0.7833 (tt0) cc_final: 0.7265 (pt0) REVERT: B 109 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 258 ASN cc_start: 0.9251 (m110) cc_final: 0.9015 (m110) REVERT: B 301 MET cc_start: 0.8190 (mtt) cc_final: 0.7953 (mtt) REVERT: B 417 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7662 (mmt-90) REVERT: B 419 ILE cc_start: 0.8783 (mm) cc_final: 0.8530 (mp) REVERT: B 427 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: B 465 ARG cc_start: 0.7837 (tmm-80) cc_final: 0.7477 (ttp80) REVERT: B 504 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5452 (t80) REVERT: C 31 GLU cc_start: 0.7688 (tt0) cc_final: 0.7116 (pt0) REVERT: C 248 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8172 (mmtp) REVERT: C 301 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7727 (mttp) REVERT: C 312 SER cc_start: 0.8380 (p) cc_final: 0.7872 (t) REVERT: C 429 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7758 (mmp-170) outliers start: 80 outliers final: 59 residues processed: 272 average time/residue: 0.1566 time to fit residues: 62.4622 Evaluate side-chains 268 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [105, 182, 47, 31, 192, 184, 206, 36, 12, 85, 110] chunk 105 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 184 optimal weight: 0.0970 chunk 206 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105048 restraints weight = 19890.758| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.76 r_work: 0.3047 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17922 Z= 0.165 Angle : 0.595 8.356 24365 Z= 0.298 Chirality : 0.046 0.337 2689 Planarity : 0.004 0.040 3099 Dihedral : 7.932 87.036 3058 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 4.40 % Allowed : 19.14 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2121 helix: 2.21 (0.28), residues: 362 sheet: -0.24 (0.25), residues: 512 loop : -1.07 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 30 TYR 0.009 0.001 TYR B 283 PHE 0.015 0.001 PHE H 100A TRP 0.012 0.001 TRP G 99 HIS 0.005 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (17870) covalent geometry : angle 0.56557 / 0.29 (24233) SS BOND : bond 0.00282 / 0.17 ( 21) SS BOND : angle 0.72642 / 0.41 ( 42) hydrogen bonds : bond 0.03749 / 2.49 ( 620) hydrogen bonds : angle 4.96715 / 3.46 ( 1698) Misc. bond : bond 0.00408 / 0.21 ( 1) link_ALPHA1-3 : bond 0.00785 / 0.37 ( 3) link_ALPHA1-3 : angle 1.26178 / 0.68 ( 9) link_BETA1-2 : bond 0.00365 / 0.17 ( 3) link_BETA1-2 : angle 0.81302 / 0.40 ( 9) link_BETA1-4 : bond 0.00401 / 0.23 ( 9) link_BETA1-4 : angle 2.73079 / 1.67 ( 27) link_BETA2-3 : bond 0.00580 / 0.27 ( 3) link_BETA2-3 : angle 5.96353 / 3.17 ( 9) link_NAG-ASN : bond 0.00607 / 0.34 ( 12) link_NAG-ASN : angle 2.87444 / 1.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8414 (p) cc_final: 0.8000 (m) REVERT: D 70 SER cc_start: 0.8438 (p) cc_final: 0.8127 (m) REVERT: I 68 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: G 70 SER cc_start: 0.8352 (p) cc_final: 0.7973 (m) REVERT: K 68 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: A 117 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7793 (mmm160) REVERT: A 146 CYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 186 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8883 (mp) REVERT: A 311 SER cc_start: 0.8368 (p) cc_final: 0.7990 (t) REVERT: A 374 TRP cc_start: 0.8961 (m-10) cc_final: 0.8648 (m-10) REVERT: B 25 GLU cc_start: 0.7782 (tt0) cc_final: 0.7286 (pt0) REVERT: B 109 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 258 ASN cc_start: 0.9259 (m110) cc_final: 0.9019 (m110) REVERT: B 417 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7747 (mmt-90) REVERT: B 427 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 465 ARG cc_start: 0.7877 (tmm-80) cc_final: 0.7534 (ttp80) REVERT: B 504 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5543 (t80) REVERT: C 31 GLU cc_start: 0.7735 (tt0) cc_final: 0.7142 (pt0) REVERT: C 248 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8181 (mmtp) REVERT: C 301 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7772 (mttp) REVERT: C 312 SER cc_start: 0.8400 (p) cc_final: 0.7890 (t) REVERT: C 429 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7815 (mmp-170) outliers start: 82 outliers final: 60 residues processed: 267 average time/residue: 0.1570 time to fit residues: 60.8915 Evaluate side-chains 265 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [125, 32, 129, 114, 176, 150, 105, 127, 48, 193, 15] chunk 125 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104560 restraints weight = 19902.661| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.77 r_work: 0.3043 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17922 Z= 0.179 Angle : 0.602 9.106 24365 Z= 0.302 Chirality : 0.046 0.339 2689 Planarity : 0.004 0.039 3099 Dihedral : 7.977 87.613 3058 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 4.40 % Allowed : 19.25 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2121 helix: 2.20 (0.28), residues: 362 sheet: -0.24 (0.24), residues: 512 loop : -1.07 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.010 0.001 TYR B 283 PHE 0.015 0.001 PHE H 100A TRP 0.013 0.001 TRP G 99 HIS 0.005 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (17870) covalent geometry : angle 0.57348 / 0.30 (24233) SS BOND : bond 0.00301 / 0.18 ( 21) SS BOND : angle 0.74321 / 0.42 ( 42) hydrogen bonds : bond 0.03782 / 2.51 ( 620) hydrogen bonds : angle 4.96907 / 3.47 ( 1698) Misc. bond : bond 0.00366 / 0.19 ( 1) link_ALPHA1-3 : bond 0.00786 / 0.37 ( 3) link_ALPHA1-3 : angle 1.26713 / 0.68 ( 9) link_BETA1-2 : bond 0.00357 / 0.17 ( 3) link_BETA1-2 : angle 0.80528 / 0.40 ( 9) link_BETA1-4 : bond 0.00412 / 0.23 ( 9) link_BETA1-4 : angle 2.74178 / 1.69 ( 27) link_BETA2-3 : bond 0.00603 / 0.28 ( 3) link_BETA2-3 : angle 6.08022 / 3.23 ( 9) link_NAG-ASN : bond 0.00549 / 0.28 ( 12) link_NAG-ASN : angle 2.83243 / 1.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 199 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8451 (p) cc_final: 0.8042 (m) REVERT: L 39 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7657 (mtm180) REVERT: D 70 SER cc_start: 0.8450 (p) cc_final: 0.8138 (m) REVERT: I 39 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7552 (mtm180) REVERT: I 68 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: G 70 SER cc_start: 0.8357 (p) cc_final: 0.7977 (m) REVERT: K 39 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7725 (mtm180) REVERT: K 68 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: A 117 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7814 (mmm160) REVERT: A 146 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7995 (m) REVERT: A 186 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8897 (mp) REVERT: A 311 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 374 TRP cc_start: 0.8966 (m-10) cc_final: 0.8637 (m-10) REVERT: B 25 GLU cc_start: 0.7781 (tt0) cc_final: 0.7293 (pt0) REVERT: B 109 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8049 (mp) REVERT: B 417 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7764 (mmt-90) REVERT: B 427 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: B 465 ARG cc_start: 0.7890 (tmm-80) cc_final: 0.7559 (ttp80) REVERT: B 504 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5601 (t80) REVERT: C 31 GLU cc_start: 0.7743 (tt0) cc_final: 0.7134 (pt0) REVERT: C 248 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8174 (mmtp) REVERT: C 301 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7798 (mttp) REVERT: C 312 SER cc_start: 0.8333 (p) cc_final: 0.7825 (t) REVERT: C 429 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7823 (mmp-170) REVERT: C 439 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7597 (mt-10) outliers start: 82 outliers final: 64 residues processed: 260 average time/residue: 0.1604 time to fit residues: 60.1058 Evaluate side-chains 275 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 199 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [22, 94, 149, 115, 112, 155, 135, 17, 176, 42, 15] chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102591 restraints weight = 19981.506| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.81 r_work: 0.3018 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17922 Z= 0.187 Angle : 0.608 9.078 24365 Z= 0.305 Chirality : 0.046 0.345 2689 Planarity : 0.004 0.039 3099 Dihedral : 8.035 88.327 3058 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 4.77 % Allowed : 18.66 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2121 helix: 2.19 (0.28), residues: 362 sheet: -0.24 (0.24), residues: 512 loop : -1.08 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.010 0.001 TYR B 283 PHE 0.017 0.002 PHE H 100A TRP 0.013 0.001 TRP G 99 HIS 0.005 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (17870) covalent geometry : angle 0.57957 / 0.30 (24233) SS BOND : bond 0.00314 / 0.19 ( 21) SS BOND : angle 0.75056 / 0.42 ( 42) hydrogen bonds : bond 0.03823 / 2.53 ( 620) hydrogen bonds : angle 4.97670 / 3.47 ( 1698) Misc. bond : bond 0.00389 / 0.20 ( 1) link_ALPHA1-3 : bond 0.00773 / 0.36 ( 3) link_ALPHA1-3 : angle 1.26156 / 0.68 ( 9) link_BETA1-2 : bond 0.00363 / 0.17 ( 3) link_BETA1-2 : angle 0.80622 / 0.40 ( 9) link_BETA1-4 : bond 0.00404 / 0.23 ( 9) link_BETA1-4 : angle 2.75896 / 1.70 ( 27) link_BETA2-3 : bond 0.00596 / 0.27 ( 3) link_BETA2-3 : angle 6.19481 / 3.29 ( 9) link_NAG-ASN : bond 0.00539 / 0.27 ( 12) link_NAG-ASN : angle 2.80145 / 1.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 197 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8450 (p) cc_final: 0.8056 (m) REVERT: L 39 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7597 (mtm180) REVERT: D 70 SER cc_start: 0.8428 (p) cc_final: 0.8073 (m) REVERT: D 86 ASP cc_start: 0.8587 (m-30) cc_final: 0.8354 (m-30) REVERT: I 39 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7607 (mtm180) REVERT: I 68 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: G 70 SER cc_start: 0.8369 (p) cc_final: 0.7984 (m) REVERT: K 39 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7732 (mtm180) REVERT: K 68 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: A 117 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7799 (mmm160) REVERT: A 146 CYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 186 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (mp) REVERT: A 311 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7953 (t) REVERT: B 25 GLU cc_start: 0.7758 (tt0) cc_final: 0.7291 (pt0) REVERT: B 109 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8033 (mp) REVERT: B 417 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7758 (mmt-90) REVERT: B 419 ILE cc_start: 0.8836 (mm) cc_final: 0.8593 (mp) REVERT: B 427 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: B 465 ARG cc_start: 0.7881 (tmm-80) cc_final: 0.7552 (ttp80) REVERT: B 504 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.5592 (t80) REVERT: C 31 GLU cc_start: 0.7773 (tt0) cc_final: 0.7139 (pt0) REVERT: C 248 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8137 (mmtp) REVERT: C 312 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.7833 (t) REVERT: C 429 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7779 (mmp-170) REVERT: C 439 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7613 (mt-10) outliers start: 89 outliers final: 72 residues processed: 263 average time/residue: 0.1584 time to fit residues: 60.2731 Evaluate side-chains 281 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [140, 88, 101, 30, 139, 173, 138, 18, 71, 31, 204] chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102836 restraints weight = 19851.237| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.81 r_work: 0.3036 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17922 Z= 0.136 Angle : 0.576 9.441 24365 Z= 0.289 Chirality : 0.045 0.329 2689 Planarity : 0.004 0.038 3099 Dihedral : 7.914 86.540 3058 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.91 % Allowed : 19.57 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2121 helix: 2.27 (0.28), residues: 362 sheet: -0.20 (0.24), residues: 512 loop : -1.02 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.013 0.001 TYR A 510 PHE 0.011 0.001 PHE H 100A TRP 0.013 0.001 TRP G 99 HIS 0.003 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17870) covalent geometry : angle 0.54854 / 0.28 (24233) SS BOND : bond 0.00278 / 0.18 ( 21) SS BOND : angle 0.71701 / 0.41 ( 42) hydrogen bonds : bond 0.03619 / 2.41 ( 620) hydrogen bonds : angle 4.90092 / 3.42 ( 1698) Misc. bond : bond 0.00373 / 0.20 ( 1) link_ALPHA1-3 : bond 0.00760 / 0.35 ( 3) link_ALPHA1-3 : angle 1.24309 / 0.67 ( 9) link_BETA1-2 : bond 0.00344 / 0.16 ( 3) link_BETA1-2 : angle 0.74159 / 0.37 ( 9) link_BETA1-4 : bond 0.00404 / 0.24 ( 9) link_BETA1-4 : angle 2.66069 / 1.64 ( 27) link_BETA2-3 : bond 0.00527 / 0.24 ( 3) link_BETA2-3 : angle 5.72247 / 3.05 ( 9) link_NAG-ASN : bond 0.00540 / 0.28 ( 12) link_NAG-ASN : angle 2.68596 / 1.54 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 211 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8447 (p) cc_final: 0.8049 (m) REVERT: L 39 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7584 (mtm180) REVERT: D 70 SER cc_start: 0.8426 (p) cc_final: 0.8107 (m) REVERT: I 39 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7592 (mtm180) REVERT: I 68 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: G 70 SER cc_start: 0.8328 (p) cc_final: 0.7949 (m) REVERT: K 39 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7731 (mtm180) REVERT: K 68 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: A 117 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7736 (mmm160) REVERT: A 186 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8867 (mp) REVERT: A 311 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7975 (t) REVERT: B 25 GLU cc_start: 0.7739 (tt0) cc_final: 0.7286 (pt0) REVERT: B 109 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 258 ASN cc_start: 0.9265 (m110) cc_final: 0.9054 (m110) REVERT: B 417 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7734 (mmt-90) REVERT: B 419 ILE cc_start: 0.8821 (mm) cc_final: 0.8580 (mp) REVERT: B 465 ARG cc_start: 0.7875 (tmm-80) cc_final: 0.7563 (ttp80) REVERT: B 504 TYR cc_start: 0.5950 (OUTLIER) cc_final: 0.5614 (t80) REVERT: C 31 GLU cc_start: 0.7743 (tt0) cc_final: 0.7110 (pt0) REVERT: C 248 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8107 (mmtp) REVERT: C 312 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7833 (t) REVERT: C 376 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: C 429 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7780 (mmp-170) outliers start: 73 outliers final: 61 residues processed: 261 average time/residue: 0.1571 time to fit residues: 59.1438 Evaluate side-chains 277 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 205 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 96 TRP Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 96 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [128, 129, 201, 195, 177, 121, 146, 21, 83, 191, 76] chunk 128 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 chunk 191 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097539 restraints weight = 20262.701| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.94 r_work: 0.2881 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17922 Z= 0.207 Angle : 0.624 9.508 24365 Z= 0.313 Chirality : 0.047 0.347 2689 Planarity : 0.004 0.039 3099 Dihedral : 8.013 88.947 3058 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.09 % Favored : 94.77 % Rotamer: Outliers : 4.40 % Allowed : 19.25 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2121 helix: 2.18 (0.28), residues: 362 sheet: -0.17 (0.25), residues: 502 loop : -1.10 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.013 0.001 TYR A 510 PHE 0.018 0.002 PHE H 100A TRP 0.013 0.002 TRP H 35A HIS 0.006 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (17870) covalent geometry : angle 0.59595 / 0.31 (24233) SS BOND : bond 0.00441 / 0.29 ( 21) SS BOND : angle 0.84421 / 0.48 ( 42) hydrogen bonds : bond 0.03901 / 2.57 ( 620) hydrogen bonds : angle 4.98699 / 3.48 ( 1698) Misc. bond : bond 0.00391 / 0.21 ( 1) link_ALPHA1-3 : bond 0.00767 / 0.36 ( 3) link_ALPHA1-3 : angle 1.25931 / 0.68 ( 9) link_BETA1-2 : bond 0.00364 / 0.17 ( 3) link_BETA1-2 : angle 0.79954 / 0.39 ( 9) link_BETA1-4 : bond 0.00408 / 0.23 ( 9) link_BETA1-4 : angle 2.79104 / 1.72 ( 27) link_BETA2-3 : bond 0.00601 / 0.27 ( 3) link_BETA2-3 : angle 6.36316 / 3.38 ( 9) link_NAG-ASN : bond 0.00498 / 0.25 ( 12) link_NAG-ASN : angle 2.73068 / 1.56 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.32 seconds wall clock time: 85 minutes 8.23 seconds (5108.23 seconds total)