Starting phenix.real_space_refine on Sun Apr 27 04:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xps_38560/04_2025/8xps_38560.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xps_38560/04_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_38560/04_2025/8xps_38560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xps_38560/04_2025/8xps_38560.map" model { file = "/net/cci-nas-00/data/ceres_data/8xps_38560/04_2025/8xps_38560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xps_38560/04_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-5669/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: 3.60, per 1000 atoms: 0.79 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: 1.64 Conformation dependent library (CDL) restraints added in 532.6 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: 0.57 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: 1.27 Time building geometry restraints manager: 1.82 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.070 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- 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 : 0.474 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: 0.2134 time to fit residues: 38.0253 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 : 0.506 ------------------------------------------------------------------------------- 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 = 0.062638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055679 restraints weight = 15379.781| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.93 r_work: 0.2952 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7922 (t0) cc_final: 0.7718 (t0) REVERT: B 76 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8197 (mmtt) REVERT: B 103 VAL cc_start: 0.8005 (m) cc_final: 0.7607 (m) REVERT: A 291 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8222 (t80) REVERT: A 360 ASP cc_start: 0.8474 (t0) cc_final: 0.8132 (t0) REVERT: A 470 GLN cc_start: 0.8349 (pt0) cc_final: 0.8131 (pt0) outliers start: 25 outliers final: 11 residues processed: 121 average time/residue: 0.1808 time to fit residues: 27.1612 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 : 0.455 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 1.9990 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: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.058724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051646 restraints weight = 15598.193| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.95 r_work: 0.2843 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4699 Z= 0.195 Angle : 0.856 10.798 6433 Z= 0.390 Chirality : 0.049 0.257 775 Planarity : 0.004 0.035 778 Dihedral : 19.181 106.729 1074 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.79 % Allowed : 14.17 % Favored : 81.04 % 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: -3.28 (0.32), residues: 542 helix: -1.24 (1.43), residues: 6 sheet: -1.00 (0.37), residues: 185 loop : -3.07 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.002 0.001 HIS A 281 PHE 0.019 0.002 PHE A 537 TYR 0.017 0.002 TYR B 80 ARG 0.008 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.01065 ( 5) link_NAG-ASN : angle 3.77412 ( 15) link_ALPHA1-6 : bond 0.01501 ( 7) link_ALPHA1-6 : angle 2.92915 ( 21) link_BETA1-4 : bond 0.01192 ( 10) link_BETA1-4 : angle 2.53700 ( 30) link_ALPHA1-3 : bond 0.01126 ( 2) link_ALPHA1-3 : angle 1.67242 ( 6) hydrogen bonds : bond 0.03750 ( 96) hydrogen bonds : angle 5.59410 ( 264) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.60253 ( 16) covalent geometry : bond 0.00425 ( 4667) covalent geometry : angle 0.80111 ( 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 116 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7970 (t0) cc_final: 0.7674 (t0) REVERT: B 76 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8193 (mmtt) REVERT: B 85 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 117 VAL cc_start: 0.9151 (t) cc_final: 0.8876 (m) REVERT: A 261 GLU cc_start: 0.8515 (tp30) cc_final: 0.8195 (tp30) REVERT: A 291 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8267 (t80) REVERT: A 360 ASP cc_start: 0.8483 (t0) cc_final: 0.8149 (t0) REVERT: A 394 ASN cc_start: 0.8730 (m110) cc_final: 0.8516 (m-40) REVERT: A 450 GLN cc_start: 0.8061 (tt0) cc_final: 0.7840 (tt0) REVERT: A 466 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: A 569 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8317 (pttm) outliers start: 23 outliers final: 10 residues processed: 105 average time/residue: 0.1695 time to fit residues: 22.5223 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 : 0.500 ------------------------------------------------------------------------------- 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 466 PHE Chi-restraints excluded: chain A residue 519 TRP 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN A 247 GLN A 332 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049536 restraints weight = 15742.610| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.92 r_work: 0.2786 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4699 Z= 0.216 Angle : 0.865 10.750 6433 Z= 0.394 Chirality : 0.049 0.279 775 Planarity : 0.004 0.035 778 Dihedral : 17.662 108.081 1072 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 5.21 % Allowed : 14.38 % Favored : 80.42 % 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: -2.81 (0.33), residues: 542 helix: 0.87 (2.09), residues: 6 sheet: -0.43 (0.39), residues: 176 loop : -2.89 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.008 0.002 HIS A 233 PHE 0.017 0.002 PHE A 537 TYR 0.017 0.002 TYR A 351 ARG 0.008 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 5) link_NAG-ASN : angle 3.77527 ( 15) link_ALPHA1-6 : bond 0.01692 ( 7) link_ALPHA1-6 : angle 3.10566 ( 21) link_BETA1-4 : bond 0.01156 ( 10) link_BETA1-4 : angle 2.70004 ( 30) link_ALPHA1-3 : bond 0.01087 ( 2) link_ALPHA1-3 : angle 1.95829 ( 6) hydrogen bonds : bond 0.03487 ( 96) hydrogen bonds : angle 5.43842 ( 264) SS BOND : bond 0.00828 ( 8) SS BOND : angle 1.39841 ( 16) covalent geometry : bond 0.00480 ( 4667) covalent geometry : angle 0.80579 ( 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 109 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8057 (t0) cc_final: 0.7660 (t0) REVERT: B 76 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8184 (mmtt) REVERT: A 261 GLU cc_start: 0.8513 (tp30) cc_final: 0.8231 (tp30) REVERT: A 291 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 360 ASP cc_start: 0.8554 (t0) cc_final: 0.8197 (t0) REVERT: A 450 GLN cc_start: 0.8115 (tt0) cc_final: 0.7862 (tt0) REVERT: A 466 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: A 569 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8371 (pttm) outliers start: 25 outliers final: 15 residues processed: 98 average time/residue: 0.1707 time to fit residues: 21.3115 Evaluate side-chains 98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 85 SER 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 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 569 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.055759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048749 restraints weight = 15768.109| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.92 r_work: 0.2765 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4699 Z= 0.216 Angle : 0.878 10.319 6433 Z= 0.399 Chirality : 0.049 0.282 775 Planarity : 0.005 0.036 778 Dihedral : 17.087 109.510 1072 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.38 % Allowed : 16.04 % Favored : 79.58 % 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: -2.63 (0.33), residues: 542 helix: 1.47 (2.29), residues: 6 sheet: -0.27 (0.39), residues: 177 loop : -2.79 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.006 0.002 HIS A 233 PHE 0.016 0.002 PHE A 537 TYR 0.014 0.001 TYR A 351 ARG 0.006 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 5) link_NAG-ASN : angle 3.76995 ( 15) link_ALPHA1-6 : bond 0.01627 ( 7) link_ALPHA1-6 : angle 3.17393 ( 21) link_BETA1-4 : bond 0.01159 ( 10) link_BETA1-4 : angle 2.67462 ( 30) link_ALPHA1-3 : bond 0.01098 ( 2) link_ALPHA1-3 : angle 1.87810 ( 6) hydrogen bonds : bond 0.03358 ( 96) hydrogen bonds : angle 5.42982 ( 264) SS BOND : bond 0.00315 ( 8) SS BOND : angle 1.47245 ( 16) covalent geometry : bond 0.00492 ( 4667) covalent geometry : angle 0.81957 ( 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 106 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8002 (t0) cc_final: 0.7640 (t0) REVERT: B 76 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8207 (mmtt) REVERT: A 261 GLU cc_start: 0.8566 (tp30) cc_final: 0.8294 (tp30) REVERT: A 291 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8247 (t80) REVERT: A 326 ASN cc_start: 0.8371 (p0) cc_final: 0.7982 (p0) REVERT: A 360 ASP cc_start: 0.8507 (t0) cc_final: 0.8136 (t0) REVERT: A 394 ASN cc_start: 0.8741 (m110) cc_final: 0.8474 (m-40) REVERT: A 466 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: A 569 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8405 (pttm) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.1655 time to fit residues: 20.9261 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 538 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 569 LYS 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: 2.9990 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049391 restraints weight = 15535.556| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.92 r_work: 0.2782 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4699 Z= 0.170 Angle : 0.865 12.234 6433 Z= 0.390 Chirality : 0.049 0.282 775 Planarity : 0.004 0.043 778 Dihedral : 16.297 110.602 1072 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.96 % Allowed : 15.83 % Favored : 80.21 % 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: -2.40 (0.34), residues: 542 helix: 1.65 (2.29), residues: 6 sheet: -0.04 (0.39), residues: 177 loop : -2.67 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.006 0.001 HIS A 233 PHE 0.017 0.002 PHE B 68 TYR 0.017 0.001 TYR B 80 ARG 0.007 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 5) link_NAG-ASN : angle 3.46704 ( 15) link_ALPHA1-6 : bond 0.01637 ( 7) link_ALPHA1-6 : angle 3.10573 ( 21) link_BETA1-4 : bond 0.01177 ( 10) link_BETA1-4 : angle 2.62214 ( 30) link_ALPHA1-3 : bond 0.01198 ( 2) link_ALPHA1-3 : angle 1.74292 ( 6) hydrogen bonds : bond 0.03053 ( 96) hydrogen bonds : angle 5.26855 ( 264) SS BOND : bond 0.00238 ( 8) SS BOND : angle 1.87761 ( 16) covalent geometry : bond 0.00380 ( 4667) covalent geometry : angle 0.80885 ( 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 107 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8070 (t0) cc_final: 0.7729 (t0) REVERT: B 76 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8288 (mmtt) REVERT: A 291 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 360 ASP cc_start: 0.8513 (t0) cc_final: 0.8153 (t0) REVERT: A 394 ASN cc_start: 0.8723 (m110) cc_final: 0.8506 (m-40) REVERT: A 450 GLN cc_start: 0.8255 (tt0) cc_final: 0.8017 (tt0) REVERT: A 466 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7888 (m-10) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.1797 time to fit residues: 22.5459 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 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 ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 overall best weight: 0.9528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048871 restraints weight = 15323.107| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.90 r_work: 0.2769 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4699 Z= 0.187 Angle : 0.882 11.008 6433 Z= 0.398 Chirality : 0.049 0.277 775 Planarity : 0.004 0.040 778 Dihedral : 15.177 110.932 1072 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.96 % Allowed : 16.88 % 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: -2.25 (0.35), residues: 542 helix: 2.16 (2.44), residues: 6 sheet: -0.06 (0.39), residues: 184 loop : -2.55 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS A 233 PHE 0.021 0.002 PHE B 68 TYR 0.018 0.001 TYR B 80 ARG 0.007 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 5) link_NAG-ASN : angle 3.45598 ( 15) link_ALPHA1-6 : bond 0.01665 ( 7) link_ALPHA1-6 : angle 2.91349 ( 21) link_BETA1-4 : bond 0.01160 ( 10) link_BETA1-4 : angle 2.67252 ( 30) link_ALPHA1-3 : bond 0.01161 ( 2) link_ALPHA1-3 : angle 1.72576 ( 6) hydrogen bonds : bond 0.03141 ( 96) hydrogen bonds : angle 5.09444 ( 264) SS BOND : bond 0.00320 ( 8) SS BOND : angle 1.64747 ( 16) covalent geometry : bond 0.00423 ( 4667) covalent geometry : angle 0.83046 ( 6345) *********************** REFINEMENT MACRO_CYCLE 7 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 105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7626 (t0) REVERT: B 76 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8328 (mmtt) REVERT: B 78 THR cc_start: 0.9004 (p) cc_final: 0.8729 (p) REVERT: A 235 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8145 (mp0) REVERT: A 291 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 360 ASP cc_start: 0.8474 (t0) cc_final: 0.8041 (t0) REVERT: A 394 ASN cc_start: 0.8782 (m110) cc_final: 0.8506 (m-40) REVERT: A 466 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7912 (m-10) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.1772 time to fit residues: 22.0046 Evaluate side-chains 97 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 476 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.049020 restraints weight = 15387.567| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.95 r_work: 0.2769 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.5220 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= 0.171 Angle : 0.860 13.729 6433 Z= 0.389 Chirality : 0.049 0.274 775 Planarity : 0.004 0.043 778 Dihedral : 14.596 111.514 1072 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.54 % Allowed : 17.92 % Favored : 78.54 % 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: -2.19 (0.35), residues: 542 helix: 1.00 (2.33), residues: 7 sheet: 0.03 (0.39), residues: 184 loop : -2.52 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.005 0.001 HIS A 233 PHE 0.022 0.002 PHE B 68 TYR 0.013 0.001 TYR A 351 ARG 0.010 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 5) link_NAG-ASN : angle 3.33716 ( 15) link_ALPHA1-6 : bond 0.01573 ( 7) link_ALPHA1-6 : angle 2.71960 ( 21) link_BETA1-4 : bond 0.01172 ( 10) link_BETA1-4 : angle 2.66083 ( 30) link_ALPHA1-3 : bond 0.01169 ( 2) link_ALPHA1-3 : angle 1.67472 ( 6) hydrogen bonds : bond 0.03031 ( 96) hydrogen bonds : angle 5.00193 ( 264) SS BOND : bond 0.00192 ( 8) SS BOND : angle 1.17286 ( 16) covalent geometry : bond 0.00387 ( 4667) covalent geometry : angle 0.81179 ( 6345) *********************** REFINEMENT MACRO_CYCLE 8 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: 17 poor density : 86 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7645 (t0) REVERT: B 76 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8349 (mmtt) REVERT: B 78 THR cc_start: 0.8995 (p) cc_final: 0.8711 (p) REVERT: A 291 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 360 ASP cc_start: 0.8500 (t0) cc_final: 0.8066 (t0) REVERT: A 466 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7876 (m-10) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.1779 time to fit residues: 21.6513 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 : 0.525 ------------------------------------------------------------------------------- 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 A residue 291 TYR Chi-restraints excluded: chain A residue 329 SER 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 538 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 600 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.048299 restraints weight = 15576.676| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.94 r_work: 0.2754 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4699 Z= 0.190 Angle : 0.866 10.006 6433 Z= 0.402 Chirality : 0.049 0.270 775 Planarity : 0.005 0.044 778 Dihedral : 14.331 111.461 1072 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.75 % Allowed : 18.12 % Favored : 78.12 % 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: -2.11 (0.35), residues: 542 helix: 1.49 (2.33), residues: 6 sheet: 0.15 (0.39), residues: 184 loop : -2.51 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.005 0.001 HIS A 233 PHE 0.021 0.002 PHE B 68 TYR 0.013 0.001 TYR A 351 ARG 0.012 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 5) link_NAG-ASN : angle 3.44378 ( 15) link_ALPHA1-6 : bond 0.01481 ( 7) link_ALPHA1-6 : angle 2.61680 ( 21) link_BETA1-4 : bond 0.01171 ( 10) link_BETA1-4 : angle 2.77267 ( 30) link_ALPHA1-3 : bond 0.01085 ( 2) link_ALPHA1-3 : angle 1.71347 ( 6) hydrogen bonds : bond 0.03089 ( 96) hydrogen bonds : angle 5.03120 ( 264) SS BOND : bond 0.00193 ( 8) SS BOND : angle 1.27496 ( 16) covalent geometry : bond 0.00436 ( 4667) covalent geometry : angle 0.81663 ( 6345) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.471 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8087 (t0) cc_final: 0.7619 (t0) REVERT: B 76 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8335 (mmtt) REVERT: B 78 THR cc_start: 0.9036 (p) cc_final: 0.8766 (p) REVERT: A 235 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8130 (mp0) REVERT: A 291 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8192 (t80) REVERT: A 360 ASP cc_start: 0.8508 (t0) cc_final: 0.8005 (t0) REVERT: A 466 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7937 (m-10) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.1695 time to fit residues: 20.4625 Evaluate side-chains 95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 A residue 291 TYR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 408 ILE 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 538 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 600 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049186 restraints weight = 15161.405| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.10 r_work: 0.2774 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4699 Z= 0.164 Angle : 0.857 10.120 6433 Z= 0.399 Chirality : 0.048 0.265 775 Planarity : 0.005 0.047 778 Dihedral : 14.014 111.899 1072 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.92 % Allowed : 18.96 % Favored : 78.12 % 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: -2.00 (0.35), residues: 542 helix: 1.59 (2.30), residues: 6 sheet: 0.26 (0.39), residues: 184 loop : -2.46 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.004 0.001 HIS A 233 PHE 0.027 0.002 PHE B 68 TYR 0.013 0.001 TYR A 351 ARG 0.014 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 5) link_NAG-ASN : angle 3.25006 ( 15) link_ALPHA1-6 : bond 0.01533 ( 7) link_ALPHA1-6 : angle 2.56939 ( 21) link_BETA1-4 : bond 0.01206 ( 10) link_BETA1-4 : angle 2.77281 ( 30) link_ALPHA1-3 : bond 0.01095 ( 2) link_ALPHA1-3 : angle 1.59002 ( 6) hydrogen bonds : bond 0.02874 ( 96) hydrogen bonds : angle 4.92324 ( 264) SS BOND : bond 0.00191 ( 8) SS BOND : angle 1.06273 ( 16) covalent geometry : bond 0.00371 ( 4667) covalent geometry : angle 0.80973 ( 6345) ********************** REFINEMENT MACRO_CYCLE 10 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 96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.529 Fit side-chains REVERT: B 73 ASP cc_start: 0.8115 (t0) cc_final: 0.7597 (t0) REVERT: B 76 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8370 (mmtt) REVERT: B 78 THR cc_start: 0.9000 (p) cc_final: 0.8742 (p) REVERT: B 86 LEU cc_start: 0.9168 (pt) cc_final: 0.8952 (pt) REVERT: A 235 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8113 (mp0) REVERT: A 291 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 360 ASP cc_start: 0.8578 (t0) cc_final: 0.8023 (t0) REVERT: A 450 GLN cc_start: 0.8224 (tt0) cc_final: 0.7951 (tt0) REVERT: A 466 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7845 (m-10) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.1716 time to fit residues: 19.5953 Evaluate side-chains 93 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 A residue 291 TYR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 370 LEU 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 538 THR Chi-restraints excluded: chain A residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049682 restraints weight = 15042.974| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.08 r_work: 0.2791 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4699 Z= 0.157 Angle : 0.846 9.865 6433 Z= 0.394 Chirality : 0.048 0.258 775 Planarity : 0.005 0.047 778 Dihedral : 13.658 111.534 1072 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.92 % Allowed : 19.17 % Favored : 77.92 % 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: -1.97 (0.35), residues: 542 helix: 1.50 (2.28), residues: 6 sheet: 0.29 (0.39), residues: 184 loop : -2.45 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.004 0.001 HIS A 233 PHE 0.028 0.002 PHE B 68 TYR 0.012 0.001 TYR A 351 ARG 0.010 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 5) link_NAG-ASN : angle 3.10211 ( 15) link_ALPHA1-6 : bond 0.01530 ( 7) link_ALPHA1-6 : angle 2.53222 ( 21) link_BETA1-4 : bond 0.01199 ( 10) link_BETA1-4 : angle 2.75758 ( 30) link_ALPHA1-3 : bond 0.01071 ( 2) link_ALPHA1-3 : angle 1.55572 ( 6) hydrogen bonds : bond 0.02879 ( 96) hydrogen bonds : angle 4.85128 ( 264) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.99493 ( 16) covalent geometry : bond 0.00352 ( 4667) covalent geometry : angle 0.80065 ( 6345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.63 seconds wall clock time: 41 minutes 53.01 seconds (2513.01 seconds total)