Starting phenix.real_space_refine on Wed Oct 9 20:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_38560.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_38560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_38560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_38560.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xps_38560/10_2024/8xps_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 3.64, per 1000 atoms: 0.80 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: 1.71 Conformation dependent library (CDL) restraints added in 771.5 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: 1.55 Time building geometry restraints manager: 1.87 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: 1.020 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.160 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- 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 4667 Z= 0.278 Angle : 0.852 11.406 6345 Z= 0.429 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.550 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: 0.2319 time to fit residues: 40.9666 Evaluate side-chains 103 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 0.9990 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: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4667 Z= 0.267 Angle : 0.818 10.844 6345 Z= 0.381 Chirality : 0.050 0.214 775 Planarity : 0.005 0.043 778 Dihedral : 21.072 108.381 1084 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 5.42 % Allowed : 12.71 % Favored : 81.88 % 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: -3.80 (0.31), residues: 542 helix: -3.32 (0.78), residues: 6 sheet: -1.55 (0.36), residues: 183 loop : -3.27 (0.27), residues: 353 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 372 *********************** 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 133 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7615 (t0) cc_final: 0.7381 (t0) REVERT: B 76 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7913 (mmtt) REVERT: B 103 VAL cc_start: 0.7995 (m) cc_final: 0.7622 (m) REVERT: A 291 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 360 ASP cc_start: 0.8036 (t0) cc_final: 0.7734 (t0) REVERT: A 470 GLN cc_start: 0.8298 (pt0) cc_final: 0.8080 (pt0) outliers start: 26 outliers final: 12 residues processed: 123 average time/residue: 0.1927 time to fit residues: 29.2989 Evaluate side-chains 105 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 477 VAL 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 26 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4667 Z= 0.219 Angle : 0.775 8.854 6345 Z= 0.362 Chirality : 0.049 0.254 775 Planarity : 0.004 0.033 778 Dihedral : 19.467 107.231 1074 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.54 % Allowed : 16.25 % 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: -3.42 (0.32), residues: 542 helix: -2.46 (1.01), residues: 6 sheet: -1.15 (0.36), residues: 185 loop : -3.11 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.001 0.001 HIS A 281 PHE 0.014 0.002 PHE A 537 TYR 0.015 0.001 TYR B 50 ARG 0.009 0.001 ARG A 242 *********************** 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 109 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7618 (t0) cc_final: 0.7402 (t0) REVERT: B 76 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8032 (mmtt) REVERT: B 85 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7255 (p) REVERT: A 291 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 360 ASP cc_start: 0.7979 (t0) cc_final: 0.7682 (t0) REVERT: A 466 PHE cc_start: 0.8100 (m-80) cc_final: 0.7548 (m-10) REVERT: A 534 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.7554 (t0) outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 0.1933 time to fit residues: 24.8984 Evaluate side-chains 97 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4667 Z= 0.206 Angle : 0.781 13.259 6345 Z= 0.359 Chirality : 0.048 0.264 775 Planarity : 0.004 0.033 778 Dihedral : 17.986 106.904 1072 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.75 % Allowed : 15.62 % 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: -3.01 (0.33), residues: 542 helix: -1.95 (1.21), residues: 6 sheet: -0.59 (0.39), residues: 176 loop : -2.96 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS A 233 PHE 0.013 0.002 PHE A 537 TYR 0.014 0.001 TYR B 50 ARG 0.009 0.001 ARG B 19 *********************** 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 103 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7595 (t0) cc_final: 0.7340 (t0) REVERT: B 76 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8071 (mmtt) REVERT: A 261 GLU cc_start: 0.7996 (tp30) cc_final: 0.7674 (tp30) REVERT: A 291 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 360 ASP cc_start: 0.7975 (t0) cc_final: 0.7705 (t0) REVERT: A 466 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7595 (m-10) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.1837 time to fit residues: 22.5628 Evaluate side-chains 95 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL 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 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 554 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 332 GLN A 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 4667 Z= 0.363 Angle : 0.842 8.070 6345 Z= 0.400 Chirality : 0.050 0.278 775 Planarity : 0.005 0.038 778 Dihedral : 17.075 107.461 1072 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 4.58 % Allowed : 15.21 % 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: -2.72 (0.33), residues: 542 helix: 0.16 (2.10), residues: 6 sheet: -0.39 (0.39), residues: 177 loop : -2.80 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 104 HIS 0.009 0.002 HIS A 233 PHE 0.020 0.003 PHE A 537 TYR 0.019 0.002 TYR A 351 ARG 0.005 0.001 ARG A 402 *********************** 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 fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7685 (t0) cc_final: 0.7384 (t0) REVERT: B 76 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8014 (mmtt) REVERT: A 261 GLU cc_start: 0.8053 (tp30) cc_final: 0.7653 (tp30) REVERT: A 291 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8145 (t80) REVERT: A 360 ASP cc_start: 0.8058 (t0) cc_final: 0.7720 (t0) REVERT: A 466 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7905 (m-10) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 0.1961 time to fit residues: 24.2699 Evaluate side-chains 99 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 518 ASN Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 600 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 247 GLN A 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4667 Z= 0.237 Angle : 0.830 13.215 6345 Z= 0.383 Chirality : 0.049 0.284 775 Planarity : 0.004 0.037 778 Dihedral : 16.348 110.140 1072 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.79 % Allowed : 16.04 % 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: -2.49 (0.34), residues: 542 helix: 0.60 (2.16), residues: 6 sheet: -0.14 (0.39), residues: 176 loop : -2.69 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.007 0.001 ARG A 402 *********************** 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 108 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7694 (t0) cc_final: 0.7392 (t0) REVERT: B 76 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8130 (mmtt) REVERT: B 78 THR cc_start: 0.8868 (p) cc_final: 0.8626 (p) REVERT: A 291 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 360 ASP cc_start: 0.7951 (t0) cc_final: 0.7626 (t0) REVERT: A 466 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7754 (m-10) outliers start: 23 outliers final: 12 residues processed: 97 average time/residue: 0.2236 time to fit residues: 27.8470 Evaluate side-chains 99 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 86 LEU 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 600 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 A 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4667 Z= 0.242 Angle : 0.836 12.674 6345 Z= 0.385 Chirality : 0.049 0.277 775 Planarity : 0.004 0.041 778 Dihedral : 15.693 110.133 1072 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.33 % Allowed : 17.29 % Favored : 79.38 % 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: -2.35 (0.34), residues: 542 helix: 0.85 (2.19), residues: 6 sheet: -0.09 (0.39), residues: 177 loop : -2.57 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.005 0.001 HIS A 233 PHE 0.021 0.002 PHE B 68 TYR 0.021 0.001 TYR B 80 ARG 0.007 0.001 ARG A 242 *********************** 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 101 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7687 (t0) cc_final: 0.7374 (t0) REVERT: B 76 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8165 (mmtt) REVERT: B 78 THR cc_start: 0.8835 (p) cc_final: 0.8564 (p) REVERT: B 113 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 235 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8041 (mm-30) REVERT: A 291 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 360 ASP cc_start: 0.7960 (t0) cc_final: 0.7632 (t0) REVERT: A 466 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7770 (m-10) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.2085 time to fit residues: 24.5737 Evaluate side-chains 95 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain B residue 107 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4667 Z= 0.203 Angle : 0.812 12.620 6345 Z= 0.374 Chirality : 0.048 0.269 775 Planarity : 0.004 0.040 778 Dihedral : 14.508 110.844 1072 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.92 % Allowed : 17.71 % Favored : 79.38 % 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: -2.20 (0.35), residues: 542 helix: 1.42 (2.22), residues: 6 sheet: 0.05 (0.40), residues: 175 loop : -2.49 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 479 HIS 0.004 0.001 HIS A 233 PHE 0.021 0.001 PHE B 68 TYR 0.013 0.001 TYR A 351 ARG 0.007 0.001 ARG A 242 *********************** 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 101 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 GLU cc_start: 0.7370 (tp30) cc_final: 0.6833 (tp30) REVERT: B 73 ASP cc_start: 0.7659 (t0) cc_final: 0.7378 (t0) REVERT: B 78 THR cc_start: 0.8783 (p) cc_final: 0.8506 (p) REVERT: B 113 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 291 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7997 (t80) REVERT: A 360 ASP cc_start: 0.7920 (t0) cc_final: 0.7583 (t0) REVERT: A 394 ASN cc_start: 0.8516 (m-40) cc_final: 0.8272 (m-40) REVERT: A 466 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: A 600 GLN cc_start: 0.6814 (pp30) cc_final: 0.6494 (pp30) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.1933 time to fit residues: 22.6048 Evaluate side-chains 91 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 466 PHE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 553 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.0010 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.3444 ------------------------------------------------------------------------------- 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 A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4667 Z= 0.196 Angle : 0.797 12.783 6345 Z= 0.374 Chirality : 0.048 0.262 775 Planarity : 0.004 0.038 778 Dihedral : 13.968 109.945 1072 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.88 % Allowed : 18.54 % 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: -1.99 (0.35), residues: 542 helix: 1.46 (2.24), residues: 6 sheet: 0.08 (0.39), residues: 188 loop : -2.36 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 504 HIS 0.004 0.001 HIS A 233 PHE 0.022 0.001 PHE B 68 TYR 0.022 0.001 TYR B 80 ARG 0.011 0.001 ARG A 242 *********************** 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 92 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: B 1 GLU cc_start: 0.7458 (tp30) cc_final: 0.7076 (tp30) REVERT: B 3 GLN cc_start: 0.7092 (mm110) cc_final: 0.6609 (mm-40) REVERT: B 73 ASP cc_start: 0.7729 (t0) cc_final: 0.7455 (t0) REVERT: B 78 THR cc_start: 0.8770 (p) cc_final: 0.8509 (p) REVERT: B 113 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 291 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 360 ASP cc_start: 0.7949 (t0) cc_final: 0.7595 (t0) REVERT: A 466 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7661 (m-10) REVERT: A 569 LYS cc_start: 0.8461 (ptmm) cc_final: 0.8117 (ptmm) REVERT: A 600 GLN cc_start: 0.6880 (pp30) cc_final: 0.6641 (pp30) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.2076 time to fit residues: 22.9470 Evaluate side-chains 89 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 113 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 370 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4667 Z= 0.211 Angle : 0.827 12.727 6345 Z= 0.389 Chirality : 0.048 0.258 775 Planarity : 0.005 0.043 778 Dihedral : 13.703 109.525 1072 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.29 % Allowed : 19.17 % 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: -1.94 (0.36), residues: 542 helix: 1.58 (2.24), residues: 6 sheet: 0.20 (0.39), residues: 184 loop : -2.35 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.004 0.001 HIS A 233 PHE 0.023 0.002 PHE B 68 TYR 0.011 0.001 TYR A 280 ARG 0.014 0.001 ARG A 242 ********************** 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 93 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7625 (t0) cc_final: 0.7372 (t0) REVERT: B 78 THR cc_start: 0.8851 (p) cc_final: 0.8636 (p) REVERT: B 113 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 291 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 360 ASP cc_start: 0.7908 (t0) cc_final: 0.7510 (t0) REVERT: A 466 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: A 569 LYS cc_start: 0.8446 (ptmm) cc_final: 0.8118 (ptmm) REVERT: A 600 GLN cc_start: 0.6866 (pp30) cc_final: 0.6646 (pp30) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.1929 time to fit residues: 21.3986 Evaluate side-chains 92 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.058323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051034 restraints weight = 15211.768| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.00 r_work: 0.2829 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4667 Z= 0.227 Angle : 0.825 12.631 6345 Z= 0.388 Chirality : 0.048 0.254 775 Planarity : 0.004 0.044 778 Dihedral : 13.419 108.895 1072 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.29 % Allowed : 18.12 % 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: -1.92 (0.36), residues: 542 helix: 1.80 (2.29), residues: 6 sheet: 0.17 (0.39), residues: 188 loop : -2.33 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS A 233 PHE 0.024 0.002 PHE B 68 TYR 0.012 0.001 TYR A 351 ARG 0.014 0.001 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.10 seconds wall clock time: 30 minutes 32.22 seconds (1832.22 seconds total)