Starting phenix.real_space_refine on Sun Aug 24 06:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekf_48120/08_2025/9ekf_48120_neut.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 93 5.16 5 C 11051 2.51 5 N 2967 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17537 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3926 Classifications: {'peptide': 491} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 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: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: 3.73, per 1000 atoms: 0.21 Number of scatterers: 17537 At special positions: 0 Unit cell: (132, 136.125, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 3426 8.00 N 2967 7.00 C 11051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 482 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 314 " distance=2.03 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 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 27 " " NAG A 602 " - " ASN A 290 " " NAG A 603 " - " ASN A 14 " " NAG A 604 " - " ASN A 488 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 298 " " NAG B 603 " - " ASN B 14 " " NAG B 604 " - " ASN B 496 " " NAG C 601 " - " ASN C 27 " " NAG C 602 " - " ASN C 298 " " NAG C 603 " - " ASN C 14 " " NAG C 604 " - " ASN C 496 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 686.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3970 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 48 sheets defined 19.8% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 4.126A pdb=" N ASP A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.927A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 374 through 393 removed outlier: 3.551A pdb=" N MET A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 460 removed outlier: 3.698A pdb=" N GLU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.776A pdb=" N TYR A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.975A pdb=" N ASP B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.897A 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 401 removed outlier: 3.646A pdb=" N MET B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 469 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.677A pdb=" N SER B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.510A pdb=" N GLN B 503 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 504 " --> pdb=" O TYR B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 504' Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.732A pdb=" N LEU B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 4.103A pdb=" N ASP C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 74 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.971A pdb=" N TRP C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.702A pdb=" N MET C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 469 Processing helix chain 'C' and resid 487 through 495 removed outlier: 3.514A pdb=" N SER C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 512 removed outlier: 4.073A pdb=" N TYR C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 506 " --> pdb=" O PRO C 502 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.553A pdb=" N GLN A 6 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.396A pdb=" N GLU A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.089A pdb=" N LEU A 45 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.740A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.500A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.500A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.536A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 210 through 213 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.341A pdb=" N GLU B 18 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'B' and resid 45 through 48 removed outlier: 7.084A pdb=" N LEU B 45 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS B 286 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.698A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 83 " --> pdb=" O MET B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.445A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU B 179 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 264 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 114 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS B 271 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 112 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.445A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 179 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.548A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AC5, first strand: chain 'C' and resid 6 through 11 removed outlier: 3.552A pdb=" N GLN C 6 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.054A pdb=" N LEU C 45 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N CYS C 286 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.667A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 83 " --> pdb=" O MET C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.512A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 179 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 264 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS C 114 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS C 271 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 112 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.512A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 179 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.542A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 210 through 213 removed outlier: 7.976A pdb=" N PHE G 100 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 167 " --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AD7, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP D 52 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE D 32 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP G 52 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE G 32 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE H 32 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1746 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: 2.88 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2877 1.31 - 1.44: 5197 1.44 - 1.57: 9751 1.57 - 1.71: 3 1.71 - 1.84: 138 Bond restraints: 17966 Sorted by residual: bond pdb=" C ILE A 166 " pdb=" O ILE A 166 " ideal model delta sigma weight residual 1.236 1.175 0.061 9.90e-03 1.02e+04 3.82e+01 bond pdb=" C PRO A 162 " pdb=" O PRO A 162 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.19e-02 7.06e+03 2.70e+01 bond pdb=" C PHE B 245 " pdb=" O PHE B 245 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" C HIS B 244 " pdb=" O HIS B 244 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.21e-02 6.83e+03 2.12e+01 bond pdb=" C ILE A 164 " pdb=" O ILE A 164 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.03e-02 9.43e+03 1.82e+01 ... (remaining 17961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 23731 2.46 - 4.93: 565 4.93 - 7.39: 57 7.39 - 9.86: 6 9.86 - 12.32: 2 Bond angle restraints: 24361 Sorted by residual: angle pdb=" N ILE B 243 " pdb=" CA ILE B 243 " pdb=" C ILE B 243 " ideal model delta sigma weight residual 108.11 98.68 9.43 1.40e+00 5.10e-01 4.54e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" N HIS C 244 " pdb=" CA HIS C 244 " pdb=" C HIS C 244 " ideal model delta sigma weight residual 110.91 117.39 -6.48 1.17e+00 7.31e-01 3.07e+01 angle pdb=" C ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 110.63 118.65 -8.02 1.48e+00 4.57e-01 2.94e+01 angle pdb=" C LYS B 380 " pdb=" N GLU B 381 " pdb=" CA GLU B 381 " ideal model delta sigma weight residual 121.54 131.78 -10.24 1.91e+00 2.74e-01 2.88e+01 ... (remaining 24356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9676 17.98 - 35.96: 1027 35.96 - 53.94: 311 53.94 - 71.92: 67 71.92 - 89.90: 32 Dihedral angle restraints: 11113 sinusoidal: 4899 harmonic: 6214 Sorted by residual: dihedral pdb=" CB CYS C 486 " pdb=" SG CYS C 486 " pdb=" SG CYS C 490 " pdb=" CB CYS C 490 " ideal model delta sinusoidal sigma weight residual 93.00 161.79 -68.79 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 478 " pdb=" SG CYS A 478 " pdb=" SG CYS A 482 " pdb=" CB CYS A 482 " ideal model delta sinusoidal sigma weight residual 93.00 158.09 -65.09 1 1.00e+01 1.00e-02 5.56e+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 93.00 158.00 -65.00 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 11110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 2656 0.214 - 0.429: 14 0.429 - 0.643: 1 0.643 - 0.858: 0 0.858 - 1.072: 1 Chirality restraints: 2672 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 -2.85 0.35 2.00e-02 2.50e+03 3.08e+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 -2.83 0.33 2.00e-02 2.50e+03 2.76e+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 2.71e+02 ... (remaining 2669 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 14 " 0.020 2.00e-02 2.50e+03 7.21e-02 6.50e+01 pdb=" CG ASN B 14 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN B 14 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN B 14 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG B 603 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 14 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" CG ASN B 14 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN B 14 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 14 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 242 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ALA B 242 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA B 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 243 " 0.020 2.00e-02 2.50e+03 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 9 1.65 - 2.46: 22 2.46 - 3.27: 16549 3.27 - 4.09: 47257 4.09 - 4.90: 85208 Warning: very small nonbonded interaction distances. Nonbonded interactions: 149045 Sorted by model distance: nonbonded pdb=" OE1 GLU A 189 " pdb=" CZ TYR D 27 " model vdw 0.836 3.260 nonbonded pdb=" OE1 GLU B 189 " pdb=" CZ TYR G 27 " model vdw 0.960 3.260 nonbonded pdb=" OE1 GLU A 189 " pdb=" CE1 TYR D 27 " model vdw 1.131 3.340 nonbonded pdb=" OE1 GLU B 189 " pdb=" CE1 TYR G 27 " model vdw 1.134 3.340 nonbonded pdb=" OE2 GLU B 189 " pdb=" OH TYR G 27 " model vdw 1.236 3.040 ... (remaining 149040 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 604)) selection = (chain 'C' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 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=0.55 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.005 0.084 18017 Z= 0.311 Angle : 0.936 23.646 24493 Z= 0.540 Chirality : 0.059 1.072 2672 Planarity : 0.006 0.064 3102 Dihedral : 16.751 89.902 7080 Min Nonbonded Distance : 0.836 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 18.36 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2121 helix: -0.16 (0.25), residues: 391 sheet: 0.09 (0.23), residues: 503 loop : -1.41 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 440 TYR 0.030 0.002 TYR A 11 PHE 0.023 0.002 PHE B 245 TRP 0.049 0.003 TRP H 100G HIS 0.009 0.002 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00509 (17966) covalent geometry : angle 0.87437 (24361) SS BOND : bond 0.00343 ( 21) SS BOND : angle 1.71419 ( 42) hydrogen bonds : bond 0.13824 ( 636) hydrogen bonds : angle 7.26580 ( 1746) link_ALPHA1-3 : bond 0.00948 ( 3) link_ALPHA1-3 : angle 0.84806 ( 9) link_BETA1-2 : bond 0.00368 ( 3) link_BETA1-2 : angle 1.44248 ( 9) link_BETA1-4 : bond 0.00502 ( 9) link_BETA1-4 : angle 3.28165 ( 27) link_BETA2-3 : bond 0.00083 ( 3) link_BETA2-3 : angle 6.64578 ( 9) link_NAG-ASN : bond 0.01355 ( 12) link_NAG-ASN : angle 7.42245 ( 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 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.7498 (mt) cc_final: 0.7269 (mm) REVERT: A 116 GLU cc_start: 0.7421 (tt0) cc_final: 0.7129 (tt0) REVERT: A 262 LYS cc_start: 0.6816 (tppt) cc_final: 0.6428 (tttp) REVERT: A 265 ASP cc_start: 0.7645 (t0) cc_final: 0.7346 (t70) REVERT: A 274 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6573 (pt0) REVERT: A 311 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7699 (mttp) REVERT: A 349 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6684 (mm110) REVERT: A 384 ASN cc_start: 0.6771 (m110) cc_final: 0.6410 (m110) REVERT: A 392 LYS cc_start: 0.6459 (mmtt) cc_final: 0.6082 (mttp) REVERT: A 440 ARG cc_start: 0.5409 (mtt90) cc_final: 0.5184 (mmm160) REVERT: A 453 TYR cc_start: 0.7029 (t80) cc_final: 0.6741 (t80) REVERT: B 58 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6766 (t0) REVERT: B 73 GLU cc_start: 0.7376 (tt0) cc_final: 0.7144 (tt0) REVERT: B 199 ILE cc_start: 0.7790 (mp) cc_final: 0.7545 (mm) REVERT: B 273 ASP cc_start: 0.7360 (t0) cc_final: 0.6707 (t70) REVERT: B 282 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6612 (pt0) REVERT: B 319 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7574 (mtmm) REVERT: B 329 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6876 (pp) REVERT: B 392 ASN cc_start: 0.6807 (m110) cc_final: 0.6442 (m110) REVERT: B 448 ARG cc_start: 0.5531 (mtt90) cc_final: 0.5230 (mmm160) REVERT: B 483 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4195 (m-80) REVERT: C 73 GLU cc_start: 0.6844 (tt0) cc_final: 0.6547 (pt0) REVERT: C 116 GLU cc_start: 0.7493 (tt0) cc_final: 0.7171 (tt0) REVERT: C 270 LYS cc_start: 0.6815 (tppt) cc_final: 0.6206 (tttm) REVERT: C 273 ASP cc_start: 0.7498 (t0) cc_final: 0.7248 (t70) REVERT: C 282 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6482 (pt0) REVERT: C 319 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7658 (mttm) REVERT: C 329 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (mp) REVERT: C 392 ASN cc_start: 0.7016 (m110) cc_final: 0.6589 (m110) REVERT: C 401 MET cc_start: 0.7635 (mmt) cc_final: 0.7432 (mmt) REVERT: C 403 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.6841 (t) REVERT: C 411 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: C 428 ASP cc_start: 0.6862 (t70) cc_final: 0.6477 (m-30) REVERT: C 451 ASP cc_start: 0.6533 (m-30) cc_final: 0.6177 (m-30) REVERT: D 89 MET cc_start: 0.8688 (tpt) cc_final: 0.8483 (tpp) REVERT: G 52 ASP cc_start: 0.8038 (t0) cc_final: 0.7456 (t0) REVERT: H 81 GLN cc_start: 0.7633 (mt0) cc_final: 0.6635 (mt0) REVERT: I 39 MET cc_start: 0.7170 (mmm) cc_final: 0.6714 (mmt) REVERT: I 45 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8167 (ptt-90) REVERT: I 70 GLU cc_start: 0.6829 (tt0) cc_final: 0.6379 (tm-30) REVERT: K 65 SER cc_start: 0.8025 (p) cc_final: 0.7704 (m) REVERT: K 70 GLU cc_start: 0.6907 (tt0) cc_final: 0.6400 (mm-30) REVERT: L 70 GLU cc_start: 0.6888 (tt0) cc_final: 0.6296 (mm-30) outliers start: 40 outliers final: 12 residues processed: 266 average time/residue: 0.7123 time to fit residues: 209.7978 Evaluate side-chains 228 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 186 ASN A 197 ASN A 384 ASN A 448 ASN B 32 HIS B 142 GLN B 186 ASN B 357 GLN B 392 ASN B 467 GLN C 6 GLN C 187 ASN C 197 ASN C 392 ASN C 404 GLN C 421 ASN C 456 ASN G 81 GLN I 27 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134053 restraints weight = 17023.626| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.45 r_work: 0.3311 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18017 Z= 0.147 Angle : 0.658 21.361 24493 Z= 0.321 Chirality : 0.050 1.068 2672 Planarity : 0.004 0.051 3102 Dihedral : 8.580 84.403 3074 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.65 % Allowed : 17.02 % Favored : 79.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.17), residues: 2121 helix: 0.51 (0.27), residues: 393 sheet: 0.34 (0.23), residues: 499 loop : -1.19 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.018 0.002 TYR D 27 PHE 0.013 0.002 PHE C 345 TRP 0.022 0.002 TRP G 33 HIS 0.008 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00332 (17966) covalent geometry : angle 0.59644 (24361) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.51208 ( 42) hydrogen bonds : bond 0.04127 ( 636) hydrogen bonds : angle 5.45953 ( 1746) link_ALPHA1-3 : bond 0.00811 ( 3) link_ALPHA1-3 : angle 1.40303 ( 9) link_BETA1-2 : bond 0.00210 ( 3) link_BETA1-2 : angle 1.40679 ( 9) link_BETA1-4 : bond 0.00357 ( 9) link_BETA1-4 : angle 3.09386 ( 27) link_BETA2-3 : bond 0.00818 ( 3) link_BETA2-3 : angle 5.25012 ( 9) link_NAG-ASN : bond 0.00666 ( 12) link_NAG-ASN : angle 6.03526 ( 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 292 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.736 Fit side-chains REVERT: A 75 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (mm) REVERT: A 311 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8795 (mttm) REVERT: A 349 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7020 (mm110) REVERT: A 384 ASN cc_start: 0.7665 (m-40) cc_final: 0.7286 (m110) REVERT: A 392 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7240 (mttp) REVERT: A 453 TYR cc_start: 0.7174 (t80) cc_final: 0.6943 (t80) REVERT: A 483 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5238 (mpt) REVERT: B 185 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 273 ASP cc_start: 0.7969 (t0) cc_final: 0.7499 (t70) REVERT: B 319 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8519 (mtmm) REVERT: B 392 ASN cc_start: 0.7803 (m-40) cc_final: 0.7429 (m110) REVERT: B 483 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4351 (m-80) REVERT: C 73 GLU cc_start: 0.8057 (tt0) cc_final: 0.7813 (pt0) REVERT: C 186 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.5907 (t0) REVERT: C 319 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8781 (mttm) REVERT: C 357 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6685 (mm110) REVERT: C 392 ASN cc_start: 0.7720 (m-40) cc_final: 0.7305 (m110) REVERT: C 400 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7155 (ttmm) REVERT: C 492 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6284 (pm20) REVERT: G 40 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6415 (mpp) REVERT: H 40 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6552 (mpp) REVERT: H 81 GLN cc_start: 0.7763 (mt0) cc_final: 0.6744 (mt0) REVERT: I 70 GLU cc_start: 0.7213 (tt0) cc_final: 0.6739 (mm-30) REVERT: I 81 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: K 65 SER cc_start: 0.8240 (p) cc_final: 0.7954 (m) REVERT: K 70 GLU cc_start: 0.7351 (tt0) cc_final: 0.6879 (mm-30) REVERT: K 81 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6735 (pt0) REVERT: L 70 GLU cc_start: 0.7413 (tt0) cc_final: 0.6861 (mm-30) REVERT: L 81 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6365 (pm20) outliers start: 68 outliers final: 26 residues processed: 273 average time/residue: 0.6619 time to fit residues: 201.6456 Evaluate side-chains 246 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 299 SER 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 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 205 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 224 ASN A 459 GLN B 197 ASN B 357 GLN C 413 ASN G 81 GLN G 99 HIS I 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134684 restraints weight = 17139.740| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.27 r_work: 0.3148 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18017 Z= 0.215 Angle : 0.706 13.448 24493 Z= 0.346 Chirality : 0.055 1.314 2672 Planarity : 0.005 0.056 3102 Dihedral : 8.529 84.414 3060 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.03 % Allowed : 16.91 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2121 helix: 0.68 (0.27), residues: 390 sheet: 0.23 (0.23), residues: 503 loop : -1.14 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 509 TYR 0.017 0.002 TYR B 168 PHE 0.017 0.003 PHE C 345 TRP 0.023 0.002 TRP D 33 HIS 0.010 0.002 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00501 (17966) covalent geometry : angle 0.65291 (24361) SS BOND : bond 0.00330 ( 21) SS BOND : angle 1.60267 ( 42) hydrogen bonds : bond 0.04400 ( 636) hydrogen bonds : angle 5.47860 ( 1746) link_ALPHA1-3 : bond 0.00500 ( 3) link_ALPHA1-3 : angle 1.48528 ( 9) link_BETA1-2 : bond 0.00254 ( 3) link_BETA1-2 : angle 1.60837 ( 9) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 3.18614 ( 27) link_BETA2-3 : bond 0.01185 ( 3) link_BETA2-3 : angle 6.10802 ( 9) link_NAG-ASN : bond 0.00746 ( 12) link_NAG-ASN : angle 5.41446 ( 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 287 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 0.743 Fit side-chains REVERT: A 25 GLU cc_start: 0.7088 (tt0) cc_final: 0.6837 (tt0) REVERT: A 75 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8588 (mm) REVERT: A 311 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8748 (mttp) REVERT: A 373 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5438 (mt-10) REVERT: A 384 ASN cc_start: 0.7777 (m-40) cc_final: 0.7381 (m110) REVERT: A 392 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7365 (mttm) REVERT: A 395 THR cc_start: 0.7844 (p) cc_final: 0.7596 (t) REVERT: A 483 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5358 (mpt) REVERT: B 12 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.5640 (t70) REVERT: B 185 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 273 ASP cc_start: 0.7921 (t0) cc_final: 0.7390 (t70) REVERT: B 301 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7361 (mmt) REVERT: B 319 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8500 (mtmm) REVERT: B 381 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: B 392 ASN cc_start: 0.7918 (m-40) cc_final: 0.7578 (m110) REVERT: B 483 TYR cc_start: 0.4779 (OUTLIER) cc_final: 0.4395 (m-80) REVERT: C 24 MET cc_start: 0.7988 (mtt) cc_final: 0.7624 (mtm) REVERT: C 186 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.6025 (t0) REVERT: C 230 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9102 (mtt) REVERT: C 319 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8766 (mttm) REVERT: C 357 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6708 (mm110) REVERT: C 392 ASN cc_start: 0.7784 (m-40) cc_final: 0.7390 (m110) REVERT: C 400 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7356 (mttp) REVERT: C 451 ASP cc_start: 0.7357 (m-30) cc_final: 0.7111 (m-30) REVERT: C 492 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6313 (pm20) REVERT: D 40 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.6715 (mpp) REVERT: G 40 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.6430 (mpp) REVERT: H 40 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.6562 (mpp) REVERT: I 70 GLU cc_start: 0.7400 (tt0) cc_final: 0.6949 (tm-30) REVERT: I 100 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: K 65 SER cc_start: 0.8260 (p) cc_final: 0.7966 (m) REVERT: K 70 GLU cc_start: 0.7403 (tt0) cc_final: 0.6936 (mm-30) REVERT: K 81 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6626 (pt0) REVERT: K 100 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: L 70 GLU cc_start: 0.7429 (tt0) cc_final: 0.6834 (mm-30) REVERT: L 81 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: L 100 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7322 (pm20) outliers start: 75 outliers final: 33 residues processed: 265 average time/residue: 0.6323 time to fit residues: 187.8578 Evaluate side-chains 256 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 132 optimal weight: 9.9990 chunk 93 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 41 HIS C 421 ASN G 81 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129736 restraints weight = 17097.485| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.56 r_work: 0.3285 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18017 Z= 0.116 Angle : 0.613 15.184 24493 Z= 0.301 Chirality : 0.048 0.876 2672 Planarity : 0.004 0.047 3102 Dihedral : 8.075 82.204 3060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.70 % Allowed : 17.71 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.17), residues: 2121 helix: 0.83 (0.27), residues: 393 sheet: 0.32 (0.23), residues: 513 loop : -1.03 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 461 TYR 0.012 0.001 TYR B 168 PHE 0.014 0.002 PHE C 245 TRP 0.020 0.001 TRP G 33 HIS 0.005 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00255 (17966) covalent geometry : angle 0.56164 (24361) SS BOND : bond 0.00209 ( 21) SS BOND : angle 2.19766 ( 42) hydrogen bonds : bond 0.03684 ( 636) hydrogen bonds : angle 5.17479 ( 1746) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.15613 ( 9) link_BETA1-2 : bond 0.00093 ( 3) link_BETA1-2 : angle 1.22365 ( 9) link_BETA1-4 : bond 0.00310 ( 9) link_BETA1-4 : angle 2.87966 ( 27) link_BETA2-3 : bond 0.00839 ( 3) link_BETA2-3 : angle 5.30404 ( 9) link_NAG-ASN : bond 0.00731 ( 12) link_NAG-ASN : angle 4.79638 ( 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 284 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7122 (tt0) cc_final: 0.6889 (tt0) REVERT: A 75 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 230 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8767 (mtt) REVERT: A 311 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8831 (mttp) REVERT: A 349 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7117 (mm110) REVERT: A 373 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5432 (mt-10) REVERT: A 384 ASN cc_start: 0.7753 (m-40) cc_final: 0.7363 (m110) REVERT: A 392 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7203 (mttt) REVERT: A 440 ARG cc_start: 0.7225 (mmm160) cc_final: 0.7006 (mmm160) REVERT: A 475 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4750 (m-80) REVERT: A 483 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5361 (mpt) REVERT: A 484 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: B 240 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7621 (t70) REVERT: B 301 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: B 392 ASN cc_start: 0.7791 (m-40) cc_final: 0.7461 (m110) REVERT: B 483 TYR cc_start: 0.4743 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: C 7 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7612 (tp) REVERT: C 24 MET cc_start: 0.7937 (mtt) cc_final: 0.7588 (mtm) REVERT: C 186 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.5863 (t0) REVERT: C 319 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8843 (mttm) REVERT: C 392 ASN cc_start: 0.7758 (m-40) cc_final: 0.7359 (m110) REVERT: C 408 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7857 (t) REVERT: C 417 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8573 (mmp80) REVERT: C 451 ASP cc_start: 0.7252 (m-30) cc_final: 0.6985 (m-30) REVERT: D 40 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.6719 (mpp) REVERT: G 40 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.6465 (mpp) REVERT: G 77 THR cc_start: 0.8497 (t) cc_final: 0.8288 (m) REVERT: H 40 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.6478 (mpp) REVERT: I 70 GLU cc_start: 0.7286 (tt0) cc_final: 0.6797 (tm-30) REVERT: I 81 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: K 65 SER cc_start: 0.8250 (p) cc_final: 0.8006 (m) REVERT: K 70 GLU cc_start: 0.7388 (tt0) cc_final: 0.6897 (mm-30) REVERT: K 81 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: L 70 GLU cc_start: 0.7445 (tt0) cc_final: 0.6883 (mm-30) REVERT: L 81 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6338 (pm20) outliers start: 69 outliers final: 30 residues processed: 262 average time/residue: 0.6529 time to fit residues: 191.1000 Evaluate side-chains 253 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET 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 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 44 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 183 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 405 ASN B 413 ASN C 357 GLN C 414 ASN G 81 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.185334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131277 restraints weight = 16981.174| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.61 r_work: 0.3282 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18017 Z= 0.122 Angle : 0.628 12.389 24493 Z= 0.306 Chirality : 0.051 1.198 2672 Planarity : 0.004 0.046 3102 Dihedral : 8.013 81.123 3060 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.33 % Allowed : 18.95 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.17), residues: 2121 helix: 0.90 (0.27), residues: 393 sheet: 0.39 (0.23), residues: 513 loop : -0.97 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 96 TYR 0.013 0.001 TYR B 168 PHE 0.010 0.002 PHE A 245 TRP 0.018 0.001 TRP D 33 HIS 0.006 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00274 (17966) covalent geometry : angle 0.57481 (24361) SS BOND : bond 0.00198 ( 21) SS BOND : angle 2.59722 ( 42) hydrogen bonds : bond 0.03662 ( 636) hydrogen bonds : angle 5.05676 ( 1746) link_ALPHA1-3 : bond 0.00769 ( 3) link_ALPHA1-3 : angle 1.15225 ( 9) link_BETA1-2 : bond 0.00072 ( 3) link_BETA1-2 : angle 1.23455 ( 9) link_BETA1-4 : bond 0.00322 ( 9) link_BETA1-4 : angle 2.85695 ( 27) link_BETA2-3 : bond 0.00791 ( 3) link_BETA2-3 : angle 5.27244 ( 9) link_NAG-ASN : bond 0.00701 ( 12) link_NAG-ASN : angle 4.78602 ( 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 276 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7003 (tt0) cc_final: 0.6779 (tt0) REVERT: A 75 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 76 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7008 (mpt180) REVERT: A 230 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8773 (mtt) REVERT: A 311 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8850 (mttp) REVERT: A 349 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7151 (mm110) REVERT: A 384 ASN cc_start: 0.7734 (m-40) cc_final: 0.7341 (m110) REVERT: A 392 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7190 (mttt) REVERT: A 395 THR cc_start: 0.7830 (p) cc_final: 0.7600 (m) REVERT: A 475 TYR cc_start: 0.5397 (OUTLIER) cc_final: 0.4767 (m-80) REVERT: A 484 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: B 240 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7688 (t70) REVERT: B 301 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7349 (mmt) REVERT: B 371 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.3682 (mt-10) REVERT: B 392 ASN cc_start: 0.7781 (m-40) cc_final: 0.7451 (m110) REVERT: B 458 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6543 (tttm) REVERT: B 483 TYR cc_start: 0.4678 (OUTLIER) cc_final: 0.4317 (m-80) REVERT: C 7 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7670 (tp) REVERT: C 24 MET cc_start: 0.7931 (mtt) cc_final: 0.7588 (mtm) REVERT: C 186 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.5823 (t0) REVERT: C 319 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8854 (mttm) REVERT: C 371 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.4965 (pm20) REVERT: C 392 ASN cc_start: 0.7754 (m-40) cc_final: 0.7364 (m110) REVERT: C 417 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.8562 (mmp80) REVERT: C 451 ASP cc_start: 0.7301 (m-30) cc_final: 0.7075 (m-30) REVERT: G 40 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.6494 (mpp) REVERT: G 77 THR cc_start: 0.8485 (t) cc_final: 0.8263 (m) REVERT: H 40 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6492 (mpp) REVERT: I 70 GLU cc_start: 0.7273 (tt0) cc_final: 0.6752 (mm-30) REVERT: I 81 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6748 (pt0) REVERT: I 100 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: K 39 MET cc_start: 0.7266 (mmt) cc_final: 0.6681 (mmt) REVERT: K 65 SER cc_start: 0.8237 (p) cc_final: 0.7992 (m) REVERT: K 70 GLU cc_start: 0.7393 (tt0) cc_final: 0.6885 (mm-30) REVERT: K 81 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6547 (pt0) REVERT: L 70 GLU cc_start: 0.7456 (tt0) cc_final: 0.6874 (mm-30) outliers start: 62 outliers final: 33 residues processed: 258 average time/residue: 0.6642 time to fit residues: 190.7559 Evaluate side-chains 259 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 204 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 405 ASN A 406 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN C 357 GLN G 81 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.185640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139144 restraints weight = 16937.943| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.28 r_work: 0.3142 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18017 Z= 0.122 Angle : 0.618 15.752 24493 Z= 0.302 Chirality : 0.048 0.868 2672 Planarity : 0.004 0.045 3102 Dihedral : 7.838 80.900 3059 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.44 % Allowed : 19.16 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.18), residues: 2121 helix: 0.92 (0.27), residues: 393 sheet: 0.35 (0.23), residues: 519 loop : -0.89 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 96 TYR 0.013 0.001 TYR B 168 PHE 0.010 0.002 PHE A 245 TRP 0.018 0.001 TRP D 33 HIS 0.007 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00275 (17966) covalent geometry : angle 0.55867 (24361) SS BOND : bond 0.00229 ( 21) SS BOND : angle 2.56895 ( 42) hydrogen bonds : bond 0.03617 ( 636) hydrogen bonds : angle 5.02504 ( 1746) link_ALPHA1-3 : bond 0.00756 ( 3) link_ALPHA1-3 : angle 1.12427 ( 9) link_BETA1-2 : bond 0.00060 ( 3) link_BETA1-2 : angle 1.19743 ( 9) link_BETA1-4 : bond 0.00324 ( 9) link_BETA1-4 : angle 2.80702 ( 27) link_BETA2-3 : bond 0.00864 ( 3) link_BETA2-3 : angle 5.23298 ( 9) link_NAG-ASN : bond 0.00820 ( 12) link_NAG-ASN : angle 5.20893 ( 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 273 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8662 (mtt) REVERT: A 311 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8732 (mttp) REVERT: A 349 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7081 (mm110) REVERT: A 384 ASN cc_start: 0.7640 (m-40) cc_final: 0.7251 (m110) REVERT: A 392 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7301 (mttt) REVERT: A 395 THR cc_start: 0.7764 (p) cc_final: 0.7552 (m) REVERT: A 475 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.4776 (m-80) REVERT: A 484 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: B 240 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7364 (t0) REVERT: B 301 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7236 (mmt) REVERT: B 371 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.3701 (mt-10) REVERT: B 392 ASN cc_start: 0.7684 (m-40) cc_final: 0.7344 (m110) REVERT: B 458 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6431 (tttm) REVERT: B 483 TYR cc_start: 0.4574 (OUTLIER) cc_final: 0.4229 (m-80) REVERT: C 7 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7684 (tp) REVERT: C 24 MET cc_start: 0.7884 (mtt) cc_final: 0.7561 (mtm) REVERT: C 186 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.5795 (t0) REVERT: C 319 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8708 (mttm) REVERT: C 371 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5145 (pm20) REVERT: C 392 ASN cc_start: 0.7663 (m-40) cc_final: 0.7276 (m110) REVERT: C 451 ASP cc_start: 0.7030 (m-30) cc_final: 0.6803 (m-30) REVERT: G 40 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.6608 (mpp) REVERT: H 40 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.6541 (mpp) REVERT: I 70 GLU cc_start: 0.7111 (tt0) cc_final: 0.6666 (mm-30) REVERT: I 100 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: K 65 SER cc_start: 0.8209 (p) cc_final: 0.7954 (m) REVERT: K 70 GLU cc_start: 0.7206 (tt0) cc_final: 0.6758 (mm-30) REVERT: K 81 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6534 (pt0) REVERT: L 70 GLU cc_start: 0.7242 (tt0) cc_final: 0.6709 (mm-30) REVERT: L 100 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7279 (pm20) outliers start: 64 outliers final: 35 residues processed: 255 average time/residue: 0.6762 time to fit residues: 192.0782 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 277 HIS A 405 ASN A 406 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 414 ASN C 357 GLN G 81 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129736 restraints weight = 16905.198| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.47 r_work: 0.3106 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18017 Z= 0.209 Angle : 0.693 13.572 24493 Z= 0.342 Chirality : 0.049 0.452 2672 Planarity : 0.005 0.054 3102 Dihedral : 8.252 83.852 3059 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.76 % Allowed : 18.89 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2121 helix: 0.81 (0.27), residues: 392 sheet: 0.28 (0.22), residues: 523 loop : -0.94 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 96 TYR 0.018 0.002 TYR B 168 PHE 0.016 0.002 PHE B 345 TRP 0.023 0.002 TRP D 33 HIS 0.009 0.002 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00491 (17966) covalent geometry : angle 0.64043 (24361) SS BOND : bond 0.00313 ( 21) SS BOND : angle 2.87780 ( 42) hydrogen bonds : bond 0.04226 ( 636) hydrogen bonds : angle 5.27529 ( 1746) link_ALPHA1-3 : bond 0.00442 ( 3) link_ALPHA1-3 : angle 1.41406 ( 9) link_BETA1-2 : bond 0.00220 ( 3) link_BETA1-2 : angle 1.52002 ( 9) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 3.11074 ( 27) link_BETA2-3 : bond 0.00936 ( 3) link_BETA2-3 : angle 6.05384 ( 9) link_NAG-ASN : bond 0.00735 ( 12) link_NAG-ASN : angle 4.71795 ( 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 285 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6237 (t70) REVERT: A 311 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8829 (mttp) REVERT: A 349 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7193 (mm110) REVERT: A 384 ASN cc_start: 0.7766 (m-40) cc_final: 0.7384 (m110) REVERT: A 392 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7287 (mttt) REVERT: A 475 TYR cc_start: 0.5454 (OUTLIER) cc_final: 0.4814 (m-80) REVERT: A 484 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: B 12 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6396 (t-90) REVERT: B 240 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7692 (t70) REVERT: B 273 ASP cc_start: 0.7943 (t0) cc_final: 0.7405 (t70) REVERT: B 301 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7590 (mmt) REVERT: B 371 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.3703 (mt-10) REVERT: B 392 ASN cc_start: 0.7931 (m-40) cc_final: 0.7612 (m110) REVERT: B 458 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6549 (tttm) REVERT: B 483 TYR cc_start: 0.4645 (OUTLIER) cc_final: 0.4271 (m-80) REVERT: C 24 MET cc_start: 0.8014 (mtt) cc_final: 0.7669 (mtm) REVERT: C 186 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.5931 (t0) REVERT: C 319 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8826 (mttm) REVERT: C 371 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5171 (pm20) REVERT: C 392 ASN cc_start: 0.7790 (m-40) cc_final: 0.7407 (m110) REVERT: D 101 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7758 (mt-10) REVERT: G 40 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.6499 (mpp) REVERT: H 40 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.6576 (mpp) REVERT: I 70 GLU cc_start: 0.7403 (tt0) cc_final: 0.6948 (tm-30) REVERT: I 100 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: K 39 MET cc_start: 0.7348 (mmt) cc_final: 0.6737 (mmt) REVERT: K 65 SER cc_start: 0.8267 (p) cc_final: 0.8001 (m) REVERT: K 70 GLU cc_start: 0.7479 (tt0) cc_final: 0.6991 (mm-30) REVERT: K 100 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: L 70 GLU cc_start: 0.7574 (tt0) cc_final: 0.6979 (mm-30) REVERT: L 100 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7319 (pm20) outliers start: 70 outliers final: 34 residues processed: 262 average time/residue: 0.6512 time to fit residues: 190.5495 Evaluate side-chains 259 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 405 ASN B 413 ASN C 357 GLN G 81 GLN H 6 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.183495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131106 restraints weight = 16997.534| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.56 r_work: 0.3107 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18017 Z= 0.156 Angle : 0.636 11.897 24493 Z= 0.315 Chirality : 0.047 0.470 2672 Planarity : 0.004 0.049 3102 Dihedral : 8.088 83.141 3059 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 19.43 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2121 helix: 0.86 (0.27), residues: 392 sheet: 0.06 (0.22), residues: 543 loop : -0.86 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 96 TYR 0.017 0.002 TYR A 11 PHE 0.011 0.002 PHE C 412 TRP 0.021 0.001 TRP D 33 HIS 0.007 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00362 (17966) covalent geometry : angle 0.58476 (24361) SS BOND : bond 0.00295 ( 21) SS BOND : angle 2.77207 ( 42) hydrogen bonds : bond 0.03866 ( 636) hydrogen bonds : angle 5.18880 ( 1746) link_ALPHA1-3 : bond 0.00714 ( 3) link_ALPHA1-3 : angle 1.24714 ( 9) link_BETA1-2 : bond 0.00136 ( 3) link_BETA1-2 : angle 1.31294 ( 9) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 2.92499 ( 27) link_BETA2-3 : bond 0.00778 ( 3) link_BETA2-3 : angle 5.65288 ( 9) link_NAG-ASN : bond 0.00794 ( 12) link_NAG-ASN : angle 4.43868 ( 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 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6228 (t70) REVERT: A 116 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: A 311 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8839 (mttp) REVERT: A 349 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7146 (mm110) REVERT: A 384 ASN cc_start: 0.7705 (m-40) cc_final: 0.7317 (m110) REVERT: A 392 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7373 (mttm) REVERT: A 475 TYR cc_start: 0.5284 (OUTLIER) cc_final: 0.4626 (m-80) REVERT: A 484 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: B 12 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6437 (t-90) REVERT: B 240 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7679 (t70) REVERT: B 301 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7453 (mmt) REVERT: B 371 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.3672 (mp0) REVERT: B 392 ASN cc_start: 0.7883 (m-40) cc_final: 0.7559 (m110) REVERT: B 458 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6476 (tttm) REVERT: B 483 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.4271 (m-80) REVERT: C 24 MET cc_start: 0.7944 (mtt) cc_final: 0.7610 (mtm) REVERT: C 186 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.5868 (t0) REVERT: C 319 LYS cc_start: 0.9118 (mtmt) cc_final: 0.8820 (mttm) REVERT: C 371 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5126 (pm20) REVERT: C 392 ASN cc_start: 0.7735 (m-40) cc_final: 0.7350 (m110) REVERT: C 492 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6296 (mm-30) REVERT: D 101 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7794 (mt-10) REVERT: G 40 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: H 40 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6533 (mpp) REVERT: I 70 GLU cc_start: 0.7285 (tt0) cc_final: 0.6800 (tm-30) REVERT: I 81 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: I 100 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: K 39 MET cc_start: 0.7344 (mmt) cc_final: 0.6733 (mmt) REVERT: K 65 SER cc_start: 0.8242 (p) cc_final: 0.8006 (m) REVERT: K 70 GLU cc_start: 0.7461 (tt0) cc_final: 0.6967 (mm-30) REVERT: L 70 GLU cc_start: 0.7476 (tt0) cc_final: 0.6832 (mm-30) REVERT: L 100 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7305 (pm20) outliers start: 60 outliers final: 33 residues processed: 253 average time/residue: 0.6847 time to fit residues: 192.7430 Evaluate side-chains 258 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 70 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 405 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS B 413 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN H 6 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.180122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126820 restraints weight = 16980.725| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.49 r_work: 0.3012 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 18017 Z= 0.282 Angle : 0.775 13.598 24493 Z= 0.383 Chirality : 0.052 0.509 2672 Planarity : 0.005 0.055 3102 Dihedral : 8.742 88.356 3057 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.22 % Allowed : 19.38 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.17), residues: 2121 helix: 0.69 (0.27), residues: 390 sheet: -0.11 (0.22), residues: 543 loop : -0.97 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 96 TYR 0.021 0.002 TYR B 168 PHE 0.021 0.003 PHE C 412 TRP 0.025 0.002 TRP H 33 HIS 0.010 0.002 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00670 (17966) covalent geometry : angle 0.71582 (24361) SS BOND : bond 0.00503 ( 21) SS BOND : angle 3.88019 ( 42) hydrogen bonds : bond 0.04633 ( 636) hydrogen bonds : angle 5.53889 ( 1746) link_ALPHA1-3 : bond 0.00276 ( 3) link_ALPHA1-3 : angle 1.63156 ( 9) link_BETA1-2 : bond 0.00352 ( 3) link_BETA1-2 : angle 1.84232 ( 9) link_BETA1-4 : bond 0.00501 ( 9) link_BETA1-4 : angle 3.41944 ( 27) link_BETA2-3 : bond 0.01095 ( 3) link_BETA2-3 : angle 6.74010 ( 9) link_NAG-ASN : bond 0.00859 ( 12) link_NAG-ASN : angle 4.76009 ( 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 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6368 (t70) REVERT: A 116 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: A 311 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8858 (mttp) REVERT: A 349 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7212 (mm110) REVERT: A 384 ASN cc_start: 0.7710 (m-40) cc_final: 0.7319 (m110) REVERT: A 392 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7255 (mttt) REVERT: A 475 TYR cc_start: 0.5360 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: A 484 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6187 (pm20) REVERT: B 273 ASP cc_start: 0.8135 (t0) cc_final: 0.7589 (t70) REVERT: B 371 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.3741 (mt-10) REVERT: B 392 ASN cc_start: 0.7953 (m-40) cc_final: 0.7629 (m110) REVERT: B 458 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6634 (tttm) REVERT: B 483 TYR cc_start: 0.4773 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: C 8 CYS cc_start: 0.6566 (m) cc_final: 0.6069 (m) REVERT: C 23 ILE cc_start: 0.7512 (mp) cc_final: 0.7056 (mm) REVERT: C 24 MET cc_start: 0.7990 (mtt) cc_final: 0.7657 (mtm) REVERT: C 186 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.5938 (t0) REVERT: C 319 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8804 (mttm) REVERT: C 371 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5222 (pm20) REVERT: C 392 ASN cc_start: 0.7739 (m-40) cc_final: 0.7361 (m110) REVERT: D 101 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7844 (mt-10) REVERT: G 40 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.6423 (mpp) REVERT: H 40 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6483 (mpp) REVERT: I 70 GLU cc_start: 0.7637 (tt0) cc_final: 0.7148 (tm-30) REVERT: I 100 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: K 39 MET cc_start: 0.7365 (mmt) cc_final: 0.6814 (mmt) REVERT: K 65 SER cc_start: 0.8229 (p) cc_final: 0.7952 (m) REVERT: K 70 GLU cc_start: 0.7628 (tt0) cc_final: 0.7095 (mm-30) REVERT: K 100 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: L 70 GLU cc_start: 0.7656 (tt0) cc_final: 0.7004 (mm-30) REVERT: L 100 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7308 (pm20) outliers start: 60 outliers final: 35 residues processed: 267 average time/residue: 0.6524 time to fit residues: 194.8606 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.5973 > 50: distance: 72 - 103: 6.555 distance: 79 - 111: 11.184 distance: 89 - 94: 24.265 distance: 90 - 120: 30.088 distance: 94 - 95: 13.385 distance: 95 - 96: 14.709 distance: 95 - 98: 9.645 distance: 96 - 97: 33.621 distance: 96 - 103: 15.287 distance: 97 - 130: 30.528 distance: 98 - 99: 25.308 distance: 99 - 100: 18.196 distance: 100 - 101: 25.515 distance: 100 - 102: 26.121 distance: 103 - 104: 6.793 distance: 104 - 105: 10.798 distance: 104 - 107: 30.267 distance: 105 - 106: 11.467 distance: 105 - 111: 25.244 distance: 106 - 138: 41.412 distance: 107 - 108: 17.305 distance: 108 - 109: 25.681 distance: 108 - 110: 25.271 distance: 111 - 112: 25.784 distance: 112 - 113: 14.197 distance: 112 - 115: 17.767 distance: 113 - 114: 19.354 distance: 113 - 120: 38.806 distance: 114 - 146: 12.531 distance: 115 - 116: 36.724 distance: 116 - 117: 7.740 distance: 117 - 118: 37.720 distance: 118 - 119: 38.881 distance: 120 - 121: 22.750 distance: 121 - 122: 18.117 distance: 121 - 124: 27.386 distance: 122 - 123: 20.220 distance: 122 - 130: 15.887 distance: 124 - 125: 36.501 distance: 125 - 126: 31.510 distance: 125 - 127: 29.952 distance: 126 - 128: 27.999 distance: 127 - 129: 24.938 distance: 128 - 129: 17.731 distance: 130 - 131: 31.107 distance: 131 - 132: 15.240 distance: 131 - 134: 21.795 distance: 132 - 133: 20.757 distance: 132 - 138: 25.201 distance: 134 - 135: 37.576 distance: 135 - 136: 32.339 distance: 136 - 137: 37.280 distance: 138 - 139: 16.167 distance: 139 - 140: 38.283 distance: 139 - 142: 26.220 distance: 140 - 141: 51.454 distance: 140 - 146: 12.960 distance: 142 - 143: 21.894 distance: 143 - 144: 33.719 distance: 143 - 145: 20.223 distance: 146 - 147: 14.085 distance: 147 - 148: 29.482 distance: 147 - 150: 40.374 distance: 148 - 149: 53.508 distance: 148 - 152: 22.074 distance: 150 - 151: 17.947 distance: 152 - 153: 45.598 distance: 153 - 154: 34.448 distance: 153 - 156: 10.192 distance: 154 - 155: 42.281 distance: 154 - 163: 4.994 distance: 156 - 157: 38.292 distance: 157 - 158: 19.009 distance: 158 - 159: 11.966 distance: 159 - 160: 7.160 distance: 160 - 161: 24.906 distance: 160 - 162: 26.258 distance: 163 - 164: 11.909 distance: 164 - 165: 37.693 distance: 164 - 167: 24.256 distance: 165 - 166: 42.197 distance: 165 - 171: 40.534 distance: 167 - 168: 43.678 distance: 167 - 169: 44.552 distance: 168 - 170: 28.802 distance: 171 - 172: 17.096 distance: 172 - 173: 10.843 distance: 172 - 175: 15.569 distance: 173 - 174: 9.573 distance: 173 - 179: 29.875 distance: 175 - 176: 21.496 distance: 176 - 177: 15.459 distance: 176 - 178: 17.734