Starting phenix.real_space_refine on Sat May 10 01:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.map" model { file = "/net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xps_38560/05_2025/8xps_38560.cif" } resolution = 3.22 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= -0.024 sd= 0.413 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2874 2.51 5 N 727 2.21 5 O 942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4568 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3376 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 402} Chain: "C" 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: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.41, per 1000 atoms: 0.75 Number of scatterers: 4568 At special positions: 0 Unit cell: (84.812, 84.812, 110.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 942 8.00 N 727 7.00 C 2874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 6 " " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 5 " " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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-ASN " NAG C 1 " - " ASN A 417 " " NAG D 1 " - " ASN A 306 " " NAG E 1 " - " ASN A 195 " " NAG F 1 " - " ASN A 529 " " NAG G 1 " - " ASN A 378 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 532.0 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 13 sheets defined 3.1% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.517A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.590A pdb=" N MET A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.627A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.572A pdb=" N SER B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 225 removed outlier: 5.994A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 247 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 225 removed outlier: 5.994A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 279 through 284 removed outlier: 5.324A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU A 314 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.836A pdb=" N MET A 349 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 363 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 356 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.836A pdb=" N MET A 349 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 442 through 447 Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 471 removed outlier: 3.667A pdb=" N GLN A 470 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 476 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.465A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 540 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 547 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 561 through 567 removed outlier: 3.532A pdb=" N SER A 576 " --> pdb=" O PHE A 593 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 264 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: 1.25 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 956 1.33 - 1.45: 1143 1.45 - 1.57: 2531 1.57 - 1.69: 3 1.69 - 1.81: 34 Bond restraints: 4667 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta sigma weight residual 1.461 1.500 -0.038 1.30e-02 5.92e+03 8.68e+00 bond pdb=" N ASN A 473 " pdb=" CA ASN A 473 " ideal model delta sigma weight residual 1.462 1.487 -0.026 9.50e-03 1.11e+04 7.35e+00 bond pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 1.528 1.582 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" N VAL A 477 " pdb=" CA VAL A 477 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.20e-02 6.94e+03 6.28e+00 ... (remaining 4662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 6169 2.28 - 4.56: 134 4.56 - 6.84: 37 6.84 - 9.12: 3 9.12 - 11.41: 2 Bond angle restraints: 6345 Sorted by residual: angle pdb=" N GLN A 470 " pdb=" CA GLN A 470 " pdb=" C GLN A 470 " ideal model delta sigma weight residual 113.88 105.95 7.93 1.23e+00 6.61e-01 4.16e+01 angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" C PRO A 474 " ideal model delta sigma weight residual 112.47 101.06 11.41 2.06e+00 2.36e-01 3.07e+01 angle pdb=" CA ASN A 478 " pdb=" C ASN A 478 " pdb=" O ASN A 478 " ideal model delta sigma weight residual 120.98 116.51 4.47 1.08e+00 8.57e-01 1.72e+01 angle pdb=" CA LEU A 475 " pdb=" C LEU A 475 " pdb=" O LEU A 475 " ideal model delta sigma weight residual 121.02 116.56 4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N PRO A 474 " pdb=" CD PRO A 474 " pdb=" CG PRO A 474 " ideal model delta sigma weight residual 103.20 98.30 4.90 1.50e+00 4.44e-01 1.07e+01 ... (remaining 6340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 2918 24.21 - 48.41: 88 48.41 - 72.62: 20 72.62 - 96.83: 47 96.83 - 121.03: 25 Dihedral angle restraints: 3098 sinusoidal: 1516 harmonic: 1582 Sorted by residual: dihedral pdb=" C ASN A 473 " pdb=" N ASN A 473 " pdb=" CA ASN A 473 " pdb=" CB ASN A 473 " ideal model delta harmonic sigma weight residual -122.60 -134.34 11.74 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" N ASN A 473 " pdb=" C ASN A 473 " pdb=" CA ASN A 473 " pdb=" CB ASN A 473 " ideal model delta harmonic sigma weight residual 122.80 133.58 -10.78 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" C2 MAN D 4 " pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " pdb=" C5 MAN D 4 " ideal model delta sinusoidal sigma weight residual -57.62 63.41 -121.03 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 3095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 684 0.087 - 0.174: 81 0.174 - 0.260: 7 0.260 - 0.347: 2 0.347 - 0.434: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA ASN A 473 " pdb=" N ASN A 473 " pdb=" C ASN A 473 " pdb=" CB ASN A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA VAL A 477 " pdb=" N VAL A 477 " pdb=" C VAL A 477 " pdb=" CB VAL A 477 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 772 not shown) Planarity restraints: 783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 473 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C ASN A 473 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 473 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO A 474 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 467 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLY A 467 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY A 467 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 468 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 473 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 474 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.022 5.00e-02 4.00e+02 ... (remaining 780 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 418 2.75 - 3.28: 4268 3.28 - 3.82: 7226 3.82 - 4.36: 8373 4.36 - 4.90: 14560 Nonbonded interactions: 34845 Sorted by model distance: nonbonded pdb=" O3 NAG G 2 " pdb=" O2 BMA G 3 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" O ASP A 257 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 454 " pdb=" O ASN A 509 " model vdw 2.289 3.040 nonbonded pdb=" O3 NAG F 2 " pdb=" O2 BMA F 3 " model vdw 2.334 3.040 nonbonded pdb=" O3 NAG D 2 " pdb=" O2 BMA D 3 " model vdw 2.348 3.040 ... (remaining 34840 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 'C' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.540 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4699 Z= 0.274 Angle : 0.872 11.406 6433 Z= 0.432 Chirality : 0.057 0.434 775 Planarity : 0.003 0.039 778 Dihedral : 20.478 121.032 2064 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.04 % Favored : 90.59 % Rotamer: Outliers : 4.58 % Allowed : 5.62 % Favored : 89.79 % Cbeta Deviations : 0.20 % 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: -4.49 (0.29), residues: 542 helix: -1.38 (2.33), residues: 6 sheet: -2.13 (0.35), residues: 173 loop : -3.70 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.001 0.000 HIS A 233 PHE 0.005 0.001 PHE A 537 TYR 0.004 0.001 TYR A 454 ARG 0.001 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 5) link_NAG-ASN : angle 1.87321 ( 15) link_ALPHA1-6 : bond 0.00709 ( 7) link_ALPHA1-6 : angle 1.43491 ( 21) link_BETA1-4 : bond 0.01105 ( 10) link_BETA1-4 : angle 2.36185 ( 30) link_ALPHA1-3 : bond 0.00454 ( 2) link_ALPHA1-3 : angle 1.61709 ( 6) hydrogen bonds : bond 0.30114 ( 96) hydrogen bonds : angle 10.72727 ( 264) SS BOND : bond 0.00096 ( 8) SS BOND : angle 0.54201 ( 16) covalent geometry : bond 0.00494 ( 4667) covalent geometry : angle 0.85211 ( 6345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8858 (mt) cc_final: 0.8345 (mt) REVERT: A 197 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8311 (tp) REVERT: A 360 ASP cc_start: 0.7905 (t0) cc_final: 0.7643 (t0) outliers start: 22 outliers final: 5 residues processed: 147 average time/residue: 0.2055 time to fit residues: 36.4435 Evaluate side-chains 103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 326 ASN A 334 GLN A 358 GLN A 394 ASN A 478 ASN A 534 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055711 restraints weight = 15370.829| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.94 r_work: 0.2953 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4699 Z= 0.196 Angle : 0.879 11.656 6433 Z= 0.396 Chirality : 0.051 0.240 775 Planarity : 0.005 0.042 778 Dihedral : 21.389 109.429 1084 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 5.21 % Allowed : 12.50 % Favored : 82.29 % 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: -3.79 (0.31), residues: 542 helix: -3.17 (0.87), residues: 6 sheet: -1.51 (0.38), residues: 175 loop : -3.26 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 573 HIS 0.001 0.000 HIS A 406 PHE 0.017 0.002 PHE A 364 TYR 0.016 0.002 TYR B 50 ARG 0.005 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.01074 ( 5) link_NAG-ASN : angle 3.84383 ( 15) link_ALPHA1-6 : bond 0.01455 ( 7) link_ALPHA1-6 : angle 2.95483 ( 21) link_BETA1-4 : bond 0.01347 ( 10) link_BETA1-4 : angle 2.93272 ( 30) link_ALPHA1-3 : bond 0.00918 ( 2) link_ALPHA1-3 : angle 2.12253 ( 6) hydrogen bonds : bond 0.04023 ( 96) hydrogen bonds : angle 6.42559 ( 264) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.51718 ( 16) covalent geometry : bond 0.00423 ( 4667) covalent geometry : angle 0.81802 ( 6345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7924 (t0) cc_final: 0.7711 (t0) REVERT: B 76 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8197 (mmtt) REVERT: B 103 VAL cc_start: 0.8013 (m) cc_final: 0.7603 (m) REVERT: A 291 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8221 (t80) REVERT: A 360 ASP cc_start: 0.8499 (t0) cc_final: 0.8134 (t0) REVERT: A 470 GLN cc_start: 0.8364 (pt0) cc_final: 0.8143 (pt0) outliers start: 25 outliers final: 11 residues processed: 121 average time/residue: 0.1809 time to fit residues: 27.2524 Evaluate side-chains 105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 553 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051814 restraints weight = 15596.252| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.95 r_work: 0.2848 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4699 Z= 0.197 Angle : 0.855 11.322 6433 Z= 0.389 Chirality : 0.049 0.254 775 Planarity : 0.004 0.035 778 Dihedral : 19.354 106.852 1074 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.38 % Allowed : 15.00 % Favored : 80.62 % 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: -3.32 (0.32), residues: 542 helix: -1.41 (1.39), residues: 6 sheet: -1.05 (0.37), residues: 185 loop : -3.08 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.002 0.001 HIS A 281 PHE 0.018 0.002 PHE A 537 TYR 0.017 0.002 TYR B 50 ARG 0.009 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 5) link_NAG-ASN : angle 3.84052 ( 15) link_ALPHA1-6 : bond 0.01591 ( 7) link_ALPHA1-6 : angle 2.96724 ( 21) link_BETA1-4 : bond 0.01144 ( 10) link_BETA1-4 : angle 2.55301 ( 30) link_ALPHA1-3 : bond 0.01109 ( 2) link_ALPHA1-3 : angle 1.72347 ( 6) hydrogen bonds : bond 0.03736 ( 96) hydrogen bonds : angle 5.64209 ( 264) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.72279 ( 16) covalent geometry : bond 0.00424 ( 4667) covalent geometry : angle 0.79716 ( 6345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7989 (t0) cc_final: 0.7686 (t0) REVERT: B 76 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8165 (mmtt) REVERT: B 85 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 117 VAL cc_start: 0.9153 (t) cc_final: 0.8882 (m) REVERT: A 261 GLU cc_start: 0.8504 (tp30) cc_final: 0.8204 (tp30) REVERT: A 291 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8270 (t80) REVERT: A 326 ASN cc_start: 0.8376 (p0) cc_final: 0.7858 (p0) REVERT: A 360 ASP cc_start: 0.8500 (t0) cc_final: 0.8137 (t0) REVERT: A 394 ASN cc_start: 0.8709 (m110) cc_final: 0.8496 (m-40) REVERT: A 450 GLN cc_start: 0.8054 (tt0) cc_final: 0.7834 (tt0) REVERT: A 466 PHE cc_start: 0.8289 (m-80) cc_final: 0.7812 (m-10) REVERT: A 534 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 569 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (pttm) outliers start: 21 outliers final: 10 residues processed: 105 average time/residue: 0.1716 time to fit residues: 22.6706 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 569 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 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 3 GLN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051243 restraints weight = 15645.637| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.94 r_work: 0.2838 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4699 Z= 0.175 Angle : 0.838 10.414 6433 Z= 0.381 Chirality : 0.048 0.272 775 Planarity : 0.004 0.034 778 Dihedral : 17.870 107.691 1072 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.00 % Allowed : 15.21 % Favored : 79.79 % 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: -2.91 (0.33), residues: 542 helix: 0.02 (1.77), residues: 6 sheet: -0.54 (0.38), residues: 184 loop : -2.96 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.002 HIS A 233 PHE 0.014 0.002 PHE A 537 TYR 0.014 0.001 TYR A 351 ARG 0.006 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 5) link_NAG-ASN : angle 3.61280 ( 15) link_ALPHA1-6 : bond 0.01720 ( 7) link_ALPHA1-6 : angle 3.05364 ( 21) link_BETA1-4 : bond 0.01156 ( 10) link_BETA1-4 : angle 2.58110 ( 30) link_ALPHA1-3 : bond 0.01143 ( 2) link_ALPHA1-3 : angle 1.82049 ( 6) hydrogen bonds : bond 0.03392 ( 96) hydrogen bonds : angle 5.35524 ( 264) SS BOND : bond 0.00671 ( 8) SS BOND : angle 1.27161 ( 16) covalent geometry : bond 0.00378 ( 4667) covalent geometry : angle 0.78185 ( 6345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7947 (t0) cc_final: 0.7568 (t0) REVERT: B 76 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8175 (mmtt) REVERT: A 291 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8236 (t80) REVERT: A 360 ASP cc_start: 0.8534 (t0) cc_final: 0.8181 (t0) REVERT: A 450 GLN cc_start: 0.8066 (tt0) cc_final: 0.7854 (tt0) REVERT: A 466 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (m-10) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.1696 time to fit residues: 21.5058 Evaluate side-chains 105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 555 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 281 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.047197 restraints weight = 16009.696| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.95 r_work: 0.2719 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 4699 Z= 0.295 Angle : 0.947 11.034 6433 Z= 0.436 Chirality : 0.051 0.277 775 Planarity : 0.005 0.038 778 Dihedral : 17.352 108.777 1072 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.58 % Allowed : 14.79 % Favored : 80.62 % 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: -2.70 (0.33), residues: 542 helix: 1.41 (2.46), residues: 6 sheet: -0.33 (0.38), residues: 177 loop : -2.83 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 104 HIS 0.008 0.002 HIS A 233 PHE 0.022 0.003 PHE B 68 TYR 0.019 0.002 TYR A 351 ARG 0.004 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 5) link_NAG-ASN : angle 4.06716 ( 15) link_ALPHA1-6 : bond 0.01538 ( 7) link_ALPHA1-6 : angle 3.19702 ( 21) link_BETA1-4 : bond 0.01179 ( 10) link_BETA1-4 : angle 2.80943 ( 30) link_ALPHA1-3 : bond 0.00965 ( 2) link_ALPHA1-3 : angle 2.04026 ( 6) hydrogen bonds : bond 0.03751 ( 96) hydrogen bonds : angle 5.55608 ( 264) SS BOND : bond 0.00341 ( 8) SS BOND : angle 1.68755 ( 16) covalent geometry : bond 0.00676 ( 4667) covalent geometry : angle 0.88746 ( 6345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8079 (t0) cc_final: 0.7695 (t0) REVERT: B 76 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8147 (mmtt) REVERT: A 261 GLU cc_start: 0.8520 (tp30) cc_final: 0.8189 (tp30) REVERT: A 291 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8271 (t80) REVERT: A 360 ASP cc_start: 0.8571 (t0) cc_final: 0.8175 (t0) REVERT: A 394 ASN cc_start: 0.8811 (m110) cc_final: 0.8606 (m-40) REVERT: A 466 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8064 (m-10) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 0.1691 time to fit residues: 21.5871 Evaluate side-chains 102 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.048109 restraints weight = 15644.198| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.91 r_work: 0.2745 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4699 Z= 0.198 Angle : 0.905 11.227 6433 Z= 0.411 Chirality : 0.051 0.285 775 Planarity : 0.004 0.040 778 Dihedral : 16.706 110.820 1072 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.75 % Allowed : 17.08 % Favored : 79.17 % 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: -2.51 (0.34), residues: 542 helix: 0.66 (2.31), residues: 7 sheet: -0.11 (0.39), residues: 176 loop : -2.74 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.007 0.002 HIS A 233 PHE 0.019 0.002 PHE B 68 TYR 0.014 0.001 TYR A 351 ARG 0.007 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 5) link_NAG-ASN : angle 3.82771 ( 15) link_ALPHA1-6 : bond 0.01588 ( 7) link_ALPHA1-6 : angle 3.14131 ( 21) link_BETA1-4 : bond 0.01209 ( 10) link_BETA1-4 : angle 2.72058 ( 30) link_ALPHA1-3 : bond 0.01135 ( 2) link_ALPHA1-3 : angle 1.81836 ( 6) hydrogen bonds : bond 0.03238 ( 96) hydrogen bonds : angle 5.45577 ( 264) SS BOND : bond 0.00224 ( 8) SS BOND : angle 2.03887 ( 16) covalent geometry : bond 0.00447 ( 4667) covalent geometry : angle 0.84523 ( 6345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8071 (t0) cc_final: 0.7721 (t0) REVERT: B 76 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8275 (mmtt) REVERT: A 291 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8256 (t80) REVERT: A 360 ASP cc_start: 0.8505 (t0) cc_final: 0.8134 (t0) REVERT: A 450 GLN cc_start: 0.8239 (tt0) cc_final: 0.7846 (tt0) REVERT: A 466 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8002 (m-10) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.1761 time to fit residues: 21.2867 Evaluate side-chains 98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 51.9876 > 50: distance: 23 - 156: 15.132 distance: 26 - 153: 14.030 distance: 39 - 145: 5.932 distance: 42 - 142: 13.869 distance: 69 - 109: 9.143 distance: 86 - 91: 12.947 distance: 91 - 92: 26.651 distance: 92 - 93: 18.276 distance: 92 - 95: 18.120 distance: 93 - 94: 16.236 distance: 93 - 97: 25.386 distance: 95 - 96: 22.019 distance: 97 - 98: 24.320 distance: 98 - 99: 12.106 distance: 98 - 101: 18.441 distance: 99 - 100: 27.141 distance: 99 - 106: 27.163 distance: 101 - 102: 10.348 distance: 102 - 103: 26.828 distance: 103 - 104: 14.861 distance: 104 - 105: 51.988 distance: 106 - 107: 12.888 distance: 107 - 110: 8.541 distance: 108 - 109: 10.470 distance: 108 - 115: 10.394 distance: 110 - 111: 15.777 distance: 111 - 112: 4.246 distance: 112 - 113: 4.033 distance: 112 - 114: 11.201 distance: 115 - 116: 4.178 distance: 116 - 117: 7.965 distance: 116 - 119: 14.043 distance: 117 - 118: 18.653 distance: 117 - 126: 13.837 distance: 119 - 120: 5.641 distance: 120 - 121: 10.543 distance: 121 - 122: 11.884 distance: 122 - 123: 10.834 distance: 123 - 124: 3.966 distance: 123 - 125: 6.570 distance: 126 - 127: 7.600 distance: 127 - 128: 4.807 distance: 127 - 130: 10.285 distance: 128 - 129: 23.585 distance: 128 - 134: 8.065 distance: 130 - 131: 8.366 distance: 130 - 132: 5.482 distance: 131 - 133: 9.902 distance: 134 - 135: 19.177 distance: 134 - 222: 10.132 distance: 135 - 136: 17.212 distance: 135 - 138: 18.449 distance: 136 - 137: 20.033 distance: 136 - 142: 9.675 distance: 137 - 219: 16.335 distance: 138 - 139: 22.098 distance: 138 - 140: 21.323 distance: 139 - 141: 9.084 distance: 142 - 143: 4.743 distance: 143 - 144: 10.499 distance: 144 - 145: 6.743 distance: 144 - 146: 12.541 distance: 146 - 147: 7.294 distance: 146 - 208: 6.410 distance: 147 - 148: 14.018 distance: 147 - 150: 17.703 distance: 148 - 149: 11.416 distance: 148 - 153: 17.795 distance: 149 - 205: 12.032 distance: 150 - 151: 10.586 distance: 150 - 152: 17.036 distance: 153 - 154: 18.661 distance: 154 - 155: 22.484 distance: 155 - 156: 21.755 distance: 155 - 157: 21.455 distance: 157 - 158: 6.227 distance: 158 - 159: 6.037 distance: 158 - 161: 4.154 distance: 159 - 166: 3.611 distance: 161 - 162: 3.666 distance: 162 - 163: 5.544 distance: 163 - 164: 3.576 distance: 163 - 165: 3.718