Starting phenix.real_space_refine on Wed Jun 18 12:57:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4j_41884/06_2025/8u4j_41884_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 128 5.16 5 C 6691 2.51 5 N 1805 2.21 5 O 2226 1.98 5 H 9582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20432 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9092 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 2 Chain: "B" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9088 Classifications: {'peptide': 600} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 2 Chain: "C" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.96, per 1000 atoms: 0.49 Number of scatterers: 20432 At special positions: 0 Unit cell: (86.005, 142.785, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 O 2226 8.00 N 1805 7.00 C 6691 6.00 H 9582 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.15 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.01 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.07 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=2.01 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.01 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.05 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.24 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.16 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.06 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.04 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.04 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.12 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 56 " distance=2.05 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 197 " distance=2.01 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 221 " distance=2.07 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 229 " distance=2.02 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 238 " distance=2.02 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.05 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 289 " distance=2.05 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 304 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 330 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 496 " distance=2.18 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 520 " distance=2.06 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 532 " distance=2.02 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 552 " distance=2.01 Simple disulfide: pdb=" SG CYS B 555 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 577 " distance=2.00 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 614 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 625 " distance=2.02 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 633 " distance=2.12 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 82 " distance=2.07 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.01 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 82 " distance=2.04 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 93 " distance=2.02 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 104 " distance=2.02 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 F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 701 " - " ASN A 495 " " NAG B 701 " - " ASN B 495 " " NAG E 1 " - " ASN A 548 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN A 473 " " NAG H 1 " - " ASN A 253 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 410 " " NAG K 1 " - " ASN A 138 " " NAG L 1 " - " ASN B 138 " " NAG M 1 " - " ASN B 253 " " NAG N 1 " - " ASN B 358 " " NAG O 1 " - " ASN B 410 " " NAG P 1 " - " ASN B 473 " " NAG Q 1 " - " ASN B 548 " " NAG R 1 " - " ASN B 576 " Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 32 sheets defined 15.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.928A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.403A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.942A pdb=" N ILE A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.242A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.598A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.623A pdb=" N SER B 79 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.622A pdb=" N ASP B 165 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.229A pdb=" N THR B 394 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'D' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.359A pdb=" N LEU A 63 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA A 90 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 65 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 149 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 238 removed outlier: 7.784A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.688A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 5.511A pdb=" N ASN A 457 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 434 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.758A pdb=" N ILE A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB4, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB5, first strand: chain 'A' and resid 605 through 608 removed outlier: 4.120A pdb=" N PHE A 605 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.340A pdb=" N SER B 38 " --> pdb=" O CYS D 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.507A pdb=" N LEU B 63 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA B 90 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 65 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY B 146 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 117 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.773A pdb=" N GLN B 274 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC5, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.521A pdb=" N CYS B 334 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.684A pdb=" N LEU B 432 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR B 459 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 434 " --> pdb=" O TYR B 459 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR B 461 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 436 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AC8, first strand: chain 'B' and resid 545 through 548 Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AD1, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AD2, first strand: chain 'B' and resid 624 through 625 Processing sheet with id=AD3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AD5, first strand: chain 'D' and resid 99 through 100 227 hydrogen bonds defined for protein. 414 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: 6.79 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9582 1.13 - 1.31: 1806 1.31 - 1.48: 4444 1.48 - 1.65: 4673 1.65 - 1.82: 144 Bond restraints: 20649 Sorted by residual: bond pdb=" ND2 ASN B 174 " pdb="HD22 ASN B 174 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE A 273 " pdb=" HZ PHE A 273 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS A 204 " pdb=" H HIS A 204 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLU A 54 " pdb=" H GLU A 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU A 434 " pdb=" H LEU A 434 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 20644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 31180 1.99 - 3.99: 3364 3.99 - 5.98: 1464 5.98 - 7.98: 802 7.98 - 9.97: 12 Bond angle restraints: 36822 Sorted by residual: angle pdb=" CA ASN A 138 " pdb=" CB ASN A 138 " pdb=" CG ASN A 138 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 117.31 -6.69 1.14e+00 7.69e-01 3.45e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.27 7.96 1.36e+00 5.41e-01 3.42e+01 angle pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N ILE B 357 " pdb=" CA ILE B 357 " pdb=" C ILE B 357 " ideal model delta sigma weight residual 110.62 116.08 -5.46 1.02e+00 9.61e-01 2.86e+01 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 9939 21.98 - 43.97: 439 43.97 - 65.95: 269 65.95 - 87.94: 81 87.94 - 109.92: 51 Dihedral angle restraints: 10779 sinusoidal: 6383 harmonic: 4396 Sorted by residual: dihedral pdb=" CB CYS B 621 " pdb=" SG CYS B 621 " pdb=" SG CYS B 633 " pdb=" CB CYS B 633 " ideal model delta sinusoidal sigma weight residual -86.00 -167.30 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS A 614 " pdb=" CB CYS A 614 " ideal model delta sinusoidal sigma weight residual 93.00 162.52 -69.52 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS D 77 " pdb=" SG CYS D 77 " pdb=" SG CYS D 93 " pdb=" CB CYS D 93 " ideal model delta sinusoidal sigma weight residual 93.00 158.06 -65.06 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 10776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1557 0.122 - 0.244: 207 0.244 - 0.366: 27 0.366 - 0.488: 7 0.488 - 0.610: 1 Chirality restraints: 1799 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.98e+01 ... (remaining 1796 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG M 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.57e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.210 2.00e-02 2.50e+03 1.52e-01 3.48e+02 pdb=" CG ASN A 138 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.039 2.00e-02 2.50e+03 pdb="HD21 ASN A 138 " -0.191 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.201 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 752 2.06 - 2.69: 25825 2.69 - 3.33: 56785 3.33 - 3.96: 74117 3.96 - 4.60: 107747 Nonbonded interactions: 265226 Sorted by model distance: nonbonded pdb=" H GLY A 364 " pdb=" HG1 THR A 399 " model vdw 1.419 2.100 nonbonded pdb=" OE2 GLU B 317 " pdb=" HZ1 LYS B 324 " model vdw 1.431 2.450 nonbonded pdb=" O TYR C 76 " pdb=" HE ARG C 103 " model vdw 1.493 2.450 nonbonded pdb=" H GLY A 364 " pdb=" OG1 THR A 399 " model vdw 1.540 2.450 nonbonded pdb=" HB3 ASN B 251 " pdb=" H PHE B 252 " model vdw 1.575 2.270 ... (remaining 265221 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' and (resid 26 through 595 or resid 604 through 634 or resid 701)) selection = (chain 'B' and (resid 26 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HB \ 2 or name HB3 or name HD21)) or resid 139 through 634 or resid 701)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.330 Extract box with map and model: 0.710 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 42.200 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.014 0.206 11181 Z= 0.842 Angle : 1.674 17.081 15266 Z= 1.031 Chirality : 0.087 0.610 1799 Planarity : 0.014 0.298 1878 Dihedral : 16.947 109.924 4966 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.22 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1281 helix: -2.74 (0.43), residues: 88 sheet: -1.36 (0.37), residues: 154 loop : 0.17 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP B 198 HIS 0.008 0.001 HIS B 570 PHE 0.056 0.004 PHE B 154 TYR 0.102 0.006 TYR A 157 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd link_NAG-ASN : bond 0.05312 ( 16) link_NAG-ASN : angle 5.93551 ( 48) link_ALPHA1-6 : bond 0.02761 ( 8) link_ALPHA1-6 : angle 4.44575 ( 24) link_BETA1-4 : bond 0.02830 ( 26) link_BETA1-4 : angle 6.39682 ( 78) link_ALPHA1-3 : bond 0.02594 ( 8) link_ALPHA1-3 : angle 3.96482 ( 24) hydrogen bonds : bond 0.21780 ( 227) hydrogen bonds : angle 8.76697 ( 414) SS BOND : bond 0.04774 ( 56) SS BOND : angle 3.68422 ( 112) covalent geometry : bond 0.01363 (11067) covalent geometry : angle 1.53954 (14980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 THR cc_start: 0.8907 (p) cc_final: 0.8668 (m) REVERT: B 251 ASN cc_start: 0.8169 (m-40) cc_final: 0.7465 (m-40) REVERT: B 331 PRO cc_start: 0.7434 (Cg_exo) cc_final: 0.6954 (Cg_endo) REVERT: D 68 ARG cc_start: 0.8468 (ttt180) cc_final: 0.7890 (tpm170) outliers start: 2 outliers final: 2 residues processed: 183 average time/residue: 0.7235 time to fit residues: 167.4222 Evaluate side-chains 97 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 410 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097069 restraints weight = 59588.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.101562 restraints weight = 29445.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.104634 restraints weight = 19077.858| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11181 Z= 0.163 Angle : 0.792 13.537 15266 Z= 0.384 Chirality : 0.049 0.319 1799 Planarity : 0.005 0.061 1878 Dihedral : 15.333 88.676 2575 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.44 % Allowed : 4.53 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1281 helix: -2.14 (0.49), residues: 94 sheet: -1.35 (0.35), residues: 172 loop : -0.10 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.009 0.001 HIS B 505 PHE 0.014 0.001 PHE B 154 TYR 0.013 0.001 TYR B 53 ARG 0.006 0.001 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 16) link_NAG-ASN : angle 3.53423 ( 48) link_ALPHA1-6 : bond 0.01102 ( 8) link_ALPHA1-6 : angle 1.92523 ( 24) link_BETA1-4 : bond 0.00955 ( 26) link_BETA1-4 : angle 3.60906 ( 78) link_ALPHA1-3 : bond 0.01053 ( 8) link_ALPHA1-3 : angle 2.18062 ( 24) hydrogen bonds : bond 0.05666 ( 227) hydrogen bonds : angle 7.73421 ( 414) SS BOND : bond 0.00435 ( 56) SS BOND : angle 1.20681 ( 112) covalent geometry : bond 0.00358 (11067) covalent geometry : angle 0.71230 (14980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.7665 (p0) cc_final: 0.7168 (p0) REVERT: C 110 PHE cc_start: 0.7664 (m-80) cc_final: 0.7290 (m-10) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.7581 time to fit residues: 96.2692 Evaluate side-chains 82 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.105635 restraints weight = 69128.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.106872 restraints weight = 31249.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.106951 restraints weight = 21773.042| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11181 Z= 0.158 Angle : 0.681 9.505 15266 Z= 0.330 Chirality : 0.048 0.223 1799 Planarity : 0.005 0.074 1878 Dihedral : 11.732 72.507 2574 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.87 % Allowed : 5.40 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1281 helix: -2.13 (0.49), residues: 94 sheet: -1.51 (0.35), residues: 162 loop : -0.36 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 474 HIS 0.006 0.001 HIS A 470 PHE 0.013 0.001 PHE B 154 TYR 0.013 0.001 TYR A 148 ARG 0.005 0.001 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 16) link_NAG-ASN : angle 2.69609 ( 48) link_ALPHA1-6 : bond 0.01253 ( 8) link_ALPHA1-6 : angle 1.96565 ( 24) link_BETA1-4 : bond 0.00765 ( 26) link_BETA1-4 : angle 2.51785 ( 78) link_ALPHA1-3 : bond 0.01168 ( 8) link_ALPHA1-3 : angle 1.58057 ( 24) hydrogen bonds : bond 0.04657 ( 227) hydrogen bonds : angle 7.12125 ( 414) SS BOND : bond 0.00309 ( 56) SS BOND : angle 0.92485 ( 112) covalent geometry : bond 0.00350 (11067) covalent geometry : angle 0.63243 (14980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 PHE cc_start: 0.7736 (m-80) cc_final: 0.7369 (m-10) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.6452 time to fit residues: 79.8265 Evaluate side-chains 79 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.142329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.098132 restraints weight = 69914.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103121 restraints weight = 32259.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.106374 restraints weight = 20665.329| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11181 Z= 0.127 Angle : 0.619 9.129 15266 Z= 0.298 Chirality : 0.047 0.229 1799 Planarity : 0.004 0.055 1878 Dihedral : 9.540 62.082 2574 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.96 % Allowed : 6.10 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1281 helix: -1.70 (0.53), residues: 84 sheet: -1.39 (0.38), residues: 148 loop : -0.38 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 474 HIS 0.004 0.001 HIS A 470 PHE 0.010 0.001 PHE A 252 TYR 0.009 0.001 TYR B 459 ARG 0.005 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 16) link_NAG-ASN : angle 2.46241 ( 48) link_ALPHA1-6 : bond 0.01231 ( 8) link_ALPHA1-6 : angle 1.88345 ( 24) link_BETA1-4 : bond 0.00570 ( 26) link_BETA1-4 : angle 2.24149 ( 78) link_ALPHA1-3 : bond 0.00977 ( 8) link_ALPHA1-3 : angle 1.94233 ( 24) hydrogen bonds : bond 0.03916 ( 227) hydrogen bonds : angle 6.74915 ( 414) SS BOND : bond 0.00261 ( 56) SS BOND : angle 0.77851 ( 112) covalent geometry : bond 0.00287 (11067) covalent geometry : angle 0.57276 (14980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 PHE cc_start: 0.7784 (m-80) cc_final: 0.7249 (m-80) outliers start: 11 outliers final: 10 residues processed: 79 average time/residue: 0.6171 time to fit residues: 66.0999 Evaluate side-chains 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.141337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.097026 restraints weight = 69935.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.101927 restraints weight = 32152.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.105169 restraints weight = 20581.645| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11181 Z= 0.139 Angle : 0.612 9.137 15266 Z= 0.297 Chirality : 0.046 0.241 1799 Planarity : 0.004 0.060 1878 Dihedral : 8.459 57.351 2574 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.22 % Allowed : 6.97 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1281 helix: -1.69 (0.54), residues: 84 sheet: -1.51 (0.38), residues: 150 loop : -0.44 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 474 HIS 0.003 0.001 HIS C 75 PHE 0.010 0.001 PHE B 447 TYR 0.009 0.001 TYR A 148 ARG 0.005 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 16) link_NAG-ASN : angle 2.38821 ( 48) link_ALPHA1-6 : bond 0.01225 ( 8) link_ALPHA1-6 : angle 1.85526 ( 24) link_BETA1-4 : bond 0.00601 ( 26) link_BETA1-4 : angle 2.01567 ( 78) link_ALPHA1-3 : bond 0.01045 ( 8) link_ALPHA1-3 : angle 1.59844 ( 24) hydrogen bonds : bond 0.03754 ( 227) hydrogen bonds : angle 6.53249 ( 414) SS BOND : bond 0.00328 ( 56) SS BOND : angle 1.19880 ( 112) covalent geometry : bond 0.00313 (11067) covalent geometry : angle 0.56700 (14980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 76 average time/residue: 0.5683 time to fit residues: 59.6091 Evaluate side-chains 74 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 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 463 ASN B 26 GLN B 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094849 restraints weight = 70537.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.099512 restraints weight = 33306.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102628 restraints weight = 21578.943| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11181 Z= 0.180 Angle : 0.628 9.137 15266 Z= 0.308 Chirality : 0.047 0.216 1799 Planarity : 0.004 0.062 1878 Dihedral : 7.732 57.331 2574 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.48 % Allowed : 6.53 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1281 helix: -1.89 (0.52), residues: 90 sheet: -1.54 (0.37), residues: 165 loop : -0.61 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.005 0.001 HIS B 374 PHE 0.013 0.001 PHE B 447 TYR 0.012 0.001 TYR B 53 ARG 0.004 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 16) link_NAG-ASN : angle 2.39214 ( 48) link_ALPHA1-6 : bond 0.01226 ( 8) link_ALPHA1-6 : angle 1.65280 ( 24) link_BETA1-4 : bond 0.00522 ( 26) link_BETA1-4 : angle 1.92337 ( 78) link_ALPHA1-3 : bond 0.00887 ( 8) link_ALPHA1-3 : angle 1.70986 ( 24) hydrogen bonds : bond 0.03914 ( 227) hydrogen bonds : angle 6.52831 ( 414) SS BOND : bond 0.00440 ( 56) SS BOND : angle 1.25355 ( 112) covalent geometry : bond 0.00411 (11067) covalent geometry : angle 0.58602 (14980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 75 average time/residue: 0.7777 time to fit residues: 81.6398 Evaluate side-chains 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.139771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.101591 restraints weight = 69501.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102265 restraints weight = 33740.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102010 restraints weight = 24982.055| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11181 Z= 0.117 Angle : 0.577 8.818 15266 Z= 0.280 Chirality : 0.045 0.209 1799 Planarity : 0.004 0.062 1878 Dihedral : 7.298 59.979 2574 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.13 % Allowed : 6.62 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1281 helix: -1.88 (0.52), residues: 90 sheet: -1.50 (0.38), residues: 160 loop : -0.57 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.011 0.001 PHE B 447 TYR 0.007 0.001 TYR B 53 ARG 0.006 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 16) link_NAG-ASN : angle 2.29517 ( 48) link_ALPHA1-6 : bond 0.01254 ( 8) link_ALPHA1-6 : angle 1.65596 ( 24) link_BETA1-4 : bond 0.00512 ( 26) link_BETA1-4 : angle 1.83742 ( 78) link_ALPHA1-3 : bond 0.00893 ( 8) link_ALPHA1-3 : angle 1.53707 ( 24) hydrogen bonds : bond 0.03449 ( 227) hydrogen bonds : angle 6.36430 ( 414) SS BOND : bond 0.00319 ( 56) SS BOND : angle 0.92082 ( 112) covalent geometry : bond 0.00266 (11067) covalent geometry : angle 0.53865 (14980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.5962 time to fit residues: 61.0487 Evaluate side-chains 75 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.139509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.099724 restraints weight = 70001.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.101390 restraints weight = 35728.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.102408 restraints weight = 23251.903| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11181 Z= 0.123 Angle : 0.566 8.658 15266 Z= 0.277 Chirality : 0.045 0.197 1799 Planarity : 0.004 0.064 1878 Dihedral : 6.997 59.535 2574 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.22 % Allowed : 6.53 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1281 helix: -1.63 (0.55), residues: 84 sheet: -1.26 (0.37), residues: 166 loop : -0.57 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.011 0.001 PHE B 447 TYR 0.007 0.001 TYR A 123 ARG 0.005 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 16) link_NAG-ASN : angle 2.26105 ( 48) link_ALPHA1-6 : bond 0.01250 ( 8) link_ALPHA1-6 : angle 1.65750 ( 24) link_BETA1-4 : bond 0.00496 ( 26) link_BETA1-4 : angle 1.78123 ( 78) link_ALPHA1-3 : bond 0.00836 ( 8) link_ALPHA1-3 : angle 1.49092 ( 24) hydrogen bonds : bond 0.03420 ( 227) hydrogen bonds : angle 6.27788 ( 414) SS BOND : bond 0.00376 ( 56) SS BOND : angle 0.81314 ( 112) covalent geometry : bond 0.00280 (11067) covalent geometry : angle 0.52949 (14980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 75 average time/residue: 0.5470 time to fit residues: 58.0386 Evaluate side-chains 77 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.138087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093716 restraints weight = 70283.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.098401 restraints weight = 33095.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.101475 restraints weight = 21420.027| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11181 Z= 0.183 Angle : 0.604 8.966 15266 Z= 0.298 Chirality : 0.045 0.199 1799 Planarity : 0.004 0.067 1878 Dihedral : 6.982 58.589 2574 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.39 % Allowed : 6.36 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1281 helix: -1.64 (0.55), residues: 84 sheet: -1.63 (0.37), residues: 164 loop : -0.68 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.004 0.001 HIS B 374 PHE 0.014 0.001 PHE B 447 TYR 0.010 0.001 TYR A 148 ARG 0.008 0.001 ARG C 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 16) link_NAG-ASN : angle 2.34316 ( 48) link_ALPHA1-6 : bond 0.01173 ( 8) link_ALPHA1-6 : angle 1.60616 ( 24) link_BETA1-4 : bond 0.00487 ( 26) link_BETA1-4 : angle 1.77127 ( 78) link_ALPHA1-3 : bond 0.00773 ( 8) link_ALPHA1-3 : angle 1.48635 ( 24) hydrogen bonds : bond 0.03765 ( 227) hydrogen bonds : angle 6.33206 ( 414) SS BOND : bond 0.00397 ( 56) SS BOND : angle 0.93139 ( 112) covalent geometry : bond 0.00426 (11067) covalent geometry : angle 0.56923 (14980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 75 average time/residue: 0.5309 time to fit residues: 56.1353 Evaluate side-chains 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.5757 > 50: distance: 53 - 145: 26.514 distance: 77 - 153: 30.399 distance: 80 - 150: 28.150 distance: 104 - 133: 30.253 distance: 107 - 130: 6.076 distance: 125 - 130: 6.488 distance: 130 - 131: 23.674 distance: 130 - 135: 24.755 distance: 131 - 132: 29.152 distance: 131 - 134: 12.986 distance: 131 - 136: 17.060 distance: 132 - 133: 26.919 distance: 132 - 140: 20.142 distance: 134 - 137: 22.466 distance: 134 - 138: 43.541 distance: 134 - 139: 41.127 distance: 140 - 141: 17.409 distance: 140 - 146: 15.480 distance: 141 - 142: 33.575 distance: 141 - 144: 4.081 distance: 141 - 147: 43.099 distance: 142 - 143: 40.786 distance: 142 - 150: 11.972 distance: 144 - 145: 17.662 distance: 144 - 148: 39.225 distance: 144 - 149: 21.295 distance: 150 - 157: 13.196 distance: 151 - 152: 11.082 distance: 151 - 154: 32.289 distance: 151 - 158: 11.410 distance: 152 - 153: 5.029 distance: 152 - 166: 22.744 distance: 154 - 155: 34.927 distance: 154 - 156: 23.928 distance: 154 - 159: 21.495 distance: 155 - 160: 16.699 distance: 155 - 161: 21.024 distance: 155 - 162: 29.705 distance: 156 - 163: 7.474 distance: 156 - 164: 9.797 distance: 156 - 165: 4.688 distance: 166 - 167: 6.547 distance: 166 - 173: 25.094 distance: 167 - 168: 24.007 distance: 167 - 170: 20.280 distance: 167 - 174: 22.082 distance: 168 - 180: 5.262 distance: 170 - 171: 23.726 distance: 170 - 172: 24.906 distance: 170 - 175: 17.381 distance: 171 - 176: 47.918 distance: 172 - 177: 23.656 distance: 172 - 178: 6.655 distance: 172 - 179: 9.714 distance: 180 - 181: 4.055 distance: 180 - 189: 7.454 distance: 181 - 182: 10.278 distance: 181 - 184: 11.434 distance: 181 - 190: 7.246 distance: 182 - 183: 30.025 distance: 182 - 197: 22.190 distance: 184 - 185: 43.015 distance: 184 - 191: 14.714 distance: 185 - 186: 39.565 distance: 185 - 193: 3.057 distance: 185 - 194: 6.778 distance: 186 - 187: 23.375 distance: 186 - 188: 24.071 distance: 188 - 195: 11.152 distance: 188 - 196: 17.537 distance: 197 - 198: 19.843 distance: 197 - 203: 60.833 distance: 198 - 199: 25.065 distance: 198 - 201: 38.742 distance: 198 - 204: 49.675 distance: 199 - 200: 40.529 distance: 199 - 207: 18.788 distance: 201 - 202: 20.355 distance: 201 - 205: 33.221 distance: 201 - 206: 17.780 distance: 202 - 403: 12.425 distance: 207 - 208: 28.820 distance: 207 - 213: 22.846 distance: 208 - 209: 16.433 distance: 208 - 211: 32.621 distance: 208 - 214: 8.552 distance: 209 - 210: 17.266 distance: 209 - 221: 18.881 distance: 211 - 212: 17.385 distance: 211 - 215: 17.035 distance: 211 - 216: 8.327 distance: 212 - 213: 23.734 distance: 212 - 217: 15.899 distance: 212 - 218: 25.114 distance: 213 - 219: 11.318 distance: 213 - 220: 32.689 distance: 221 - 222: 6.797 distance: 221 - 230: 6.081 distance: 222 - 223: 9.033 distance: 222 - 225: 7.018 distance: 222 - 231: 18.597 distance: 223 - 238: 29.415 distance: 225 - 226: 10.178 distance: 225 - 232: 30.673 distance: 225 - 233: 16.563 distance: 226 - 227: 10.288 distance: 226 - 234: 25.779 distance: 226 - 235: 15.615 distance: 227 - 228: 12.840 distance: 227 - 229: 14.714 distance: 229 - 236: 11.098 distance: 229 - 237: 12.099 distance: 238 - 239: 24.533 distance: 238 - 245: 19.624 distance: 239 - 240: 22.142 distance: 239 - 242: 32.808 distance: 239 - 246: 15.642 distance: 240 - 241: 14.505 distance: 240 - 252: 23.345 distance: 242 - 243: 24.943 distance: 242 - 244: 16.433 distance: 242 - 247: 6.798 distance: 243 - 248: 23.136 distance: 252 - 253: 10.807 distance: 252 - 263: 19.628 distance: 253 - 254: 7.308 distance: 253 - 256: 27.676 distance: 253 - 264: 43.297 distance: 254 - 255: 20.677 distance: 254 - 272: 14.396 distance: 256 - 257: 18.325 distance: 256 - 265: 26.572 distance: 256 - 266: 10.522 distance: 257 - 258: 26.864 distance: 258 - 260: 25.065 distance: 258 - 267: 13.371 distance: 259 - 268: 20.373 distance: 260 - 262: 13.944 distance: 260 - 269: 13.884 distance: 261 - 262: 29.344 distance: 261 - 270: 13.942 distance: 262 - 271: 7.952 distance: 272 - 310: 3.435 distance: 275 - 307: 3.352