Starting phenix.real_space_refine on Thu May 15 11:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvk_47209/05_2025/9dvk_47209_trim.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 4412 2.51 5 N 1015 2.21 5 O 1057 1.98 5 H 6319 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12839 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6292 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 13, 'TRANS': 364} Chain breaks: 2 Chain: "B" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 6364 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain breaks: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'CLR': 1, 'CPL': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'CPL': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.89, per 1000 atoms: 0.54 Number of scatterers: 12839 At special positions: 0 Unit cell: (73.4695, 72.644, 118.047, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 4 15.00 O 1057 8.00 N 1015 7.00 C 4412 6.00 H 6319 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 897.4 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.401A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.031A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.512A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 3.998A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.023A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 231 through 259 Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.932A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 removed outlier: 4.177A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.603A pdb=" N ARG B 371 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.598A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.670A pdb=" N TYR B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.064A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.148A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 618 removed outlier: 4.358A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix 468 hydrogen bonds defined for protein. 1404 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: 4.72 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6303 1.03 - 1.23: 26 1.23 - 1.42: 2968 1.42 - 1.62: 3704 1.62 - 1.81: 48 Bond restraints: 13049 Sorted by residual: bond pdb=" O3P CPL A 803 " pdb=" P CPL A 803 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O3P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O4P CPL A 803 " pdb=" P CPL A 803 " ideal model delta sigma weight residual 1.648 1.714 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O4P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.648 1.713 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N TRP B 534 " pdb=" H TRP B 534 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.04e+00 ... (remaining 13044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 23275 3.05 - 6.09: 72 6.09 - 9.14: 10 9.14 - 12.19: 6 12.19 - 15.24: 2 Bond angle restraints: 23365 Sorted by residual: angle pdb=" O1P CPL A 803 " pdb=" P CPL A 803 " pdb=" O2P CPL A 803 " ideal model delta sigma weight residual 119.55 134.79 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" O1P CPL B 802 " pdb=" P CPL B 802 " pdb=" O2P CPL B 802 " ideal model delta sigma weight residual 119.55 134.72 -15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CA TYR B 352 " pdb=" C TYR B 352 " pdb=" O TYR B 352 " ideal model delta sigma weight residual 119.97 115.46 4.51 1.15e+00 7.56e-01 1.54e+01 angle pdb=" CA TRP B 534 " pdb=" C TRP B 534 " pdb=" O TRP B 534 " ideal model delta sigma weight residual 120.42 116.51 3.91 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N TYR A 352 " pdb=" CA TYR A 352 " pdb=" C TYR A 352 " ideal model delta sigma weight residual 111.71 107.60 4.11 1.15e+00 7.56e-01 1.28e+01 ... (remaining 23360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 5995 32.51 - 65.01: 260 65.01 - 97.52: 16 97.52 - 130.02: 2 130.02 - 162.53: 4 Dihedral angle restraints: 6277 sinusoidal: 3264 harmonic: 3013 Sorted by residual: dihedral pdb=" C3 CPL A 803 " pdb=" C1 CPL A 803 " pdb=" C2 CPL A 803 " pdb=" O3P CPL A 803 " ideal model delta sinusoidal sigma weight residual 72.09 -90.44 162.53 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O2 CPL A 803 " pdb=" C1 CPL A 803 " pdb=" C2 CPL A 803 " pdb=" O3P CPL A 803 " ideal model delta sinusoidal sigma weight residual 309.18 148.89 160.29 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -68.45 140.54 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 6274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 908 0.073 - 0.147: 72 0.147 - 0.220: 0 0.220 - 0.294: 1 0.294 - 0.367: 6 Chirality restraints: 987 Sorted by residual: chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C2 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C3 CPL B 802 " pdb=" O2 CPL B 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2 CPL A 803 " pdb=" C1 CPL A 803 " pdb=" C3 CPL A 803 " pdb=" O2 CPL A 803 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 984 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 479 " 0.095 2.00e-02 2.50e+03 9.73e-02 1.42e+02 pdb=" CG ASN A 479 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 479 " -0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 479 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN A 479 " 0.148 2.00e-02 2.50e+03 pdb="HD22 ASN A 479 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 482 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" N TYR A 483 " -0.043 2.00e-02 2.50e+03 pdb=" CA TYR A 483 " 0.011 2.00e-02 2.50e+03 pdb=" H TYR A 483 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 534 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C TRP B 534 " -0.042 2.00e-02 2.50e+03 pdb=" O TRP B 534 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 535 " 0.015 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1000 2.21 - 2.81: 26695 2.81 - 3.41: 37827 3.41 - 4.00: 47721 4.00 - 4.60: 73888 Nonbonded interactions: 187131 Sorted by model distance: nonbonded pdb=" HB2 GLU B 550 " pdb="HD21 LEU B 617 " model vdw 1.618 2.440 nonbonded pdb="HH12 ARG A 548 " pdb=" OE2 GLU A 613 " model vdw 1.661 2.450 nonbonded pdb=" OG SER A 402 " pdb=" HE ARG A 604 " model vdw 1.668 2.450 nonbonded pdb="HH12 ARG B 466 " pdb=" O GLY B 621 " model vdw 1.692 2.450 nonbonded pdb="HD21 ASN B 361 " pdb=" HG1 THR B 363 " model vdw 1.717 2.100 ... (remaining 187126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 230 through 625 or resid 801)) selection = (chain 'B' and (resid 230 through 258 or (resid 265 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name \ HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD1 \ 1 or name HD12 or name HD13)) or resid 266 through 625 or resid 801)) } 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.120 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.004 0.107 6732 Z= 0.224 Angle : 0.676 15.237 9132 Z= 0.319 Chirality : 0.044 0.367 987 Planarity : 0.003 0.029 1093 Dihedral : 17.965 162.531 2437 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.74 % Allowed : 15.16 % Favored : 84.10 % 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: 3.52 (0.30), residues: 750 helix: 3.29 (0.20), residues: 584 sheet: None (None), residues: 0 loop : -1.53 (0.39), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 573 HIS 0.003 0.001 HIS B 616 PHE 0.017 0.001 PHE B 322 TYR 0.037 0.001 TYR A 352 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.09876 ( 468) hydrogen bonds : angle 4.38584 ( 1404) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.36117 ( 4) covalent geometry : bond 0.00432 ( 6730) covalent geometry : angle 0.67648 ( 9128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ASN cc_start: 0.7238 (t0) cc_final: 0.6854 (m-40) REVERT: A 468 ARG cc_start: 0.6795 (ttt180) cc_final: 0.6528 (ttm170) REVERT: A 471 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7562 (tppt) REVERT: A 624 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7258 (mtm-85) REVERT: B 272 TYR cc_start: 0.7642 (m-80) cc_final: 0.7294 (m-80) REVERT: B 318 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5958 (mm-30) REVERT: B 347 TYR cc_start: 0.7030 (m-80) cc_final: 0.6725 (m-80) REVERT: B 354 PHE cc_start: 0.8291 (t80) cc_final: 0.7979 (t80) REVERT: B 394 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5295 (p90) REVERT: B 465 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7842 (tpt170) outliers start: 5 outliers final: 4 residues processed: 143 average time/residue: 0.3853 time to fit residues: 72.9202 Evaluate side-chains 114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 58 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.189597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159271 restraints weight = 22641.439| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.33 r_work: 0.3763 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6732 Z= 0.123 Angle : 0.463 4.195 9132 Z= 0.252 Chirality : 0.035 0.135 987 Planarity : 0.004 0.040 1093 Dihedral : 15.183 156.389 1033 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.63 % Allowed : 16.79 % Favored : 81.58 % 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: 3.41 (0.30), residues: 750 helix: 3.19 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 573 HIS 0.005 0.001 HIS A 476 PHE 0.012 0.001 PHE A 605 TYR 0.014 0.001 TYR B 445 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 468) hydrogen bonds : angle 3.92970 ( 1404) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.91803 ( 4) covalent geometry : bond 0.00249 ( 6730) covalent geometry : angle 0.46286 ( 9128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7400 (m-10) cc_final: 0.7150 (m-10) REVERT: A 468 ARG cc_start: 0.6360 (ttt180) cc_final: 0.6050 (ttm170) REVERT: A 624 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7329 (mtm-85) REVERT: B 272 TYR cc_start: 0.7465 (m-80) cc_final: 0.7146 (m-80) REVERT: B 318 GLU cc_start: 0.6548 (mt-10) cc_final: 0.5720 (mm-30) REVERT: B 354 PHE cc_start: 0.8376 (t80) cc_final: 0.7870 (t80) REVERT: B 538 ASP cc_start: 0.7263 (t0) cc_final: 0.7048 (t70) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.4062 time to fit residues: 61.5806 Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN B 248 ASN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148927 restraints weight = 22709.020| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.36 r_work: 0.3621 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6732 Z= 0.149 Angle : 0.484 4.751 9132 Z= 0.265 Chirality : 0.036 0.134 987 Planarity : 0.004 0.037 1093 Dihedral : 14.672 158.535 1031 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.38 % Allowed : 15.60 % Favored : 82.02 % 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: 3.15 (0.30), residues: 750 helix: 3.00 (0.20), residues: 593 sheet: None (None), residues: 0 loop : -1.83 (0.40), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 327 HIS 0.006 0.001 HIS A 476 PHE 0.021 0.001 PHE A 605 TYR 0.011 0.001 TYR A 483 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 468) hydrogen bonds : angle 3.98863 ( 1404) SS BOND : bond 0.00410 ( 2) SS BOND : angle 0.97431 ( 4) covalent geometry : bond 0.00330 ( 6730) covalent geometry : angle 0.48323 ( 9128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7666 (m-10) cc_final: 0.7383 (m-10) REVERT: A 417 TYR cc_start: 0.7642 (t80) cc_final: 0.6311 (m-80) REVERT: A 468 ARG cc_start: 0.6566 (ttt180) cc_final: 0.6254 (ttm170) REVERT: A 550 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6603 (mt-10) REVERT: A 553 TYR cc_start: 0.7216 (m-10) cc_final: 0.6936 (m-10) REVERT: A 624 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7393 (mtm-85) REVERT: B 318 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6033 (mm-30) REVERT: B 347 TYR cc_start: 0.7255 (m-80) cc_final: 0.6719 (m-80) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.4315 time to fit residues: 60.1116 Evaluate side-chains 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143577 restraints weight = 22734.092| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.32 r_work: 0.3556 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6732 Z= 0.150 Angle : 0.489 4.370 9132 Z= 0.270 Chirality : 0.036 0.136 987 Planarity : 0.004 0.035 1093 Dihedral : 14.298 157.229 1027 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.12 % Allowed : 14.86 % Favored : 82.02 % 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: 2.90 (0.30), residues: 750 helix: 2.86 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.05 (0.37), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 327 HIS 0.005 0.001 HIS A 476 PHE 0.024 0.002 PHE B 605 TYR 0.012 0.001 TYR B 518 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 468) hydrogen bonds : angle 4.01051 ( 1404) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.01054 ( 4) covalent geometry : bond 0.00328 ( 6730) covalent geometry : angle 0.48895 ( 9128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7848 (m-10) cc_final: 0.7587 (m-10) REVERT: A 468 ARG cc_start: 0.6674 (ttt180) cc_final: 0.6268 (ttm170) REVERT: A 550 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6761 (mt-10) REVERT: A 624 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7220 (mtm-85) REVERT: B 293 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.6518 (ttm170) REVERT: B 565 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (pp20) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.4157 time to fit residues: 57.8175 Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 ASN ** 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 = 0.4002 r_free = 0.4002 target = 0.174553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143328 restraints weight = 22819.815| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.32 r_work: 0.3565 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6732 Z= 0.133 Angle : 0.475 5.271 9132 Z= 0.259 Chirality : 0.035 0.133 987 Planarity : 0.004 0.035 1093 Dihedral : 13.742 146.771 1027 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.67 % Allowed : 15.30 % Favored : 82.02 % 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: 3.03 (0.30), residues: 750 helix: 2.95 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 573 HIS 0.004 0.001 HIS B 499 PHE 0.020 0.001 PHE A 605 TYR 0.011 0.001 TYR B 518 ARG 0.008 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 468) hydrogen bonds : angle 3.95732 ( 1404) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.00760 ( 4) covalent geometry : bond 0.00283 ( 6730) covalent geometry : angle 0.47414 ( 9128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7858 (m-10) cc_final: 0.7593 (m-10) REVERT: A 468 ARG cc_start: 0.6653 (ttt180) cc_final: 0.6259 (ttm170) REVERT: A 504 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6411 (m-70) REVERT: A 550 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6801 (mt-10) REVERT: A 624 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7265 (mtm-85) REVERT: B 293 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.6517 (ttm170) REVERT: B 347 TYR cc_start: 0.7350 (m-80) cc_final: 0.6738 (m-80) REVERT: B 442 LYS cc_start: 0.8172 (tptm) cc_final: 0.7930 (mptt) outliers start: 18 outliers final: 14 residues processed: 105 average time/residue: 0.5031 time to fit residues: 67.8451 Evaluate side-chains 107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145273 restraints weight = 22920.672| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.29 r_work: 0.3561 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6732 Z= 0.117 Angle : 0.457 5.137 9132 Z= 0.250 Chirality : 0.035 0.133 987 Planarity : 0.003 0.036 1093 Dihedral : 12.986 132.102 1027 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.42 % Allowed : 14.86 % Favored : 81.72 % 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: 3.11 (0.30), residues: 750 helix: 3.00 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.96 (0.38), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 266 HIS 0.004 0.001 HIS B 499 PHE 0.017 0.001 PHE A 605 TYR 0.011 0.001 TYR B 518 ARG 0.003 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 468) hydrogen bonds : angle 3.88243 ( 1404) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.03505 ( 4) covalent geometry : bond 0.00245 ( 6730) covalent geometry : angle 0.45632 ( 9128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7833 (m-10) cc_final: 0.7565 (m-10) REVERT: A 468 ARG cc_start: 0.6551 (ttt180) cc_final: 0.6224 (ttm170) REVERT: A 504 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6297 (m90) REVERT: A 544 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: A 550 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6827 (mt-10) REVERT: A 624 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7318 (mtm-85) REVERT: B 293 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.6510 (ttm170) REVERT: B 347 TYR cc_start: 0.7326 (m-80) cc_final: 0.6735 (m-80) REVERT: B 442 LYS cc_start: 0.8165 (tptm) cc_final: 0.7881 (mptt) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.4564 time to fit residues: 64.5710 Evaluate side-chains 112 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142798 restraints weight = 22989.172| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.30 r_work: 0.3534 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6732 Z= 0.141 Angle : 0.482 5.733 9132 Z= 0.261 Chirality : 0.035 0.133 987 Planarity : 0.004 0.045 1093 Dihedral : 12.504 108.252 1027 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.27 % Allowed : 14.71 % Favored : 82.02 % 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 (0.30), residues: 750 helix: 2.93 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 528 HIS 0.004 0.001 HIS A 476 PHE 0.020 0.001 PHE A 605 TYR 0.011 0.001 TYR B 518 ARG 0.005 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 468) hydrogen bonds : angle 3.93982 ( 1404) SS BOND : bond 0.00389 ( 2) SS BOND : angle 1.05218 ( 4) covalent geometry : bond 0.00309 ( 6730) covalent geometry : angle 0.48195 ( 9128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7840 (m-10) cc_final: 0.7580 (m-10) REVERT: A 468 ARG cc_start: 0.6570 (ttt180) cc_final: 0.6262 (ttm170) REVERT: A 504 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.5932 (m90) REVERT: A 544 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6936 (m-40) REVERT: A 550 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6796 (mt-10) REVERT: A 624 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7362 (mtm-85) REVERT: B 314 GLN cc_start: 0.5773 (mt0) cc_final: 0.5301 (mm-40) REVERT: B 347 TYR cc_start: 0.7357 (m-80) cc_final: 0.6750 (m-80) REVERT: B 442 LYS cc_start: 0.8171 (tptm) cc_final: 0.7843 (mptt) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.4273 time to fit residues: 61.0136 Evaluate side-chains 116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.173689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142826 restraints weight = 23038.989| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.32 r_work: 0.3538 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6732 Z= 0.130 Angle : 0.469 5.477 9132 Z= 0.258 Chirality : 0.035 0.133 987 Planarity : 0.003 0.036 1093 Dihedral : 12.182 96.627 1027 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.97 % Allowed : 15.16 % Favored : 81.87 % 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: 2.99 (0.30), residues: 750 helix: 2.92 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 528 HIS 0.013 0.001 HIS A 441 PHE 0.022 0.001 PHE A 511 TYR 0.010 0.001 TYR B 518 ARG 0.004 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 468) hydrogen bonds : angle 3.91198 ( 1404) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.01880 ( 4) covalent geometry : bond 0.00279 ( 6730) covalent geometry : angle 0.46821 ( 9128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7840 (m-10) cc_final: 0.7599 (m-10) REVERT: A 468 ARG cc_start: 0.6579 (ttt180) cc_final: 0.6247 (ttm170) REVERT: A 471 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7573 (tppt) REVERT: A 504 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6060 (m90) REVERT: A 544 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.7021 (m-40) REVERT: A 550 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6908 (mt-10) REVERT: A 624 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7429 (mtm-85) REVERT: B 314 GLN cc_start: 0.5829 (mt0) cc_final: 0.5353 (mm-40) REVERT: B 347 TYR cc_start: 0.7323 (m-80) cc_final: 0.6706 (m-80) REVERT: B 442 LYS cc_start: 0.8173 (tptm) cc_final: 0.7826 (mptt) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.4508 time to fit residues: 62.5937 Evaluate side-chains 113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.170340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139510 restraints weight = 22825.803| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.17 r_work: 0.3503 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6732 Z= 0.170 Angle : 0.509 4.636 9132 Z= 0.279 Chirality : 0.036 0.133 987 Planarity : 0.004 0.037 1093 Dihedral : 12.128 101.035 1027 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.53 % Allowed : 15.60 % Favored : 81.87 % 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: 2.76 (0.30), residues: 750 helix: 2.74 (0.20), residues: 593 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 573 HIS 0.010 0.001 HIS A 441 PHE 0.025 0.002 PHE B 605 TYR 0.012 0.002 TYR B 518 ARG 0.004 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05427 ( 468) hydrogen bonds : angle 4.06098 ( 1404) SS BOND : bond 0.00454 ( 2) SS BOND : angle 1.12775 ( 4) covalent geometry : bond 0.00388 ( 6730) covalent geometry : angle 0.50826 ( 9128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.6560 (ttt180) cc_final: 0.6279 (ttm170) REVERT: A 471 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7576 (tppt) REVERT: A 504 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6277 (m90) REVERT: A 550 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6954 (mt-10) REVERT: A 624 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7480 (mtm-85) REVERT: B 314 GLN cc_start: 0.5840 (mt0) cc_final: 0.5378 (mm-40) REVERT: B 442 LYS cc_start: 0.8134 (tptm) cc_final: 0.7835 (mptt) outliers start: 17 outliers final: 15 residues processed: 105 average time/residue: 0.4525 time to fit residues: 61.2902 Evaluate side-chains 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** 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 = 0.3973 r_free = 0.3973 target = 0.172089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141508 restraints weight = 22688.718| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.18 r_work: 0.3527 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6732 Z= 0.128 Angle : 0.473 4.664 9132 Z= 0.262 Chirality : 0.035 0.133 987 Planarity : 0.004 0.035 1093 Dihedral : 11.679 97.063 1025 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.08 % Allowed : 16.05 % Favored : 81.87 % 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: 2.89 (0.30), residues: 750 helix: 2.85 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 528 HIS 0.010 0.001 HIS A 441 PHE 0.026 0.001 PHE A 487 TYR 0.018 0.001 TYR B 518 ARG 0.004 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 468) hydrogen bonds : angle 3.96117 ( 1404) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.11107 ( 4) covalent geometry : bond 0.00275 ( 6730) covalent geometry : angle 0.47268 ( 9128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.6535 (ttt180) cc_final: 0.6266 (ttm170) REVERT: A 471 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7540 (tppt) REVERT: A 504 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6228 (m90) REVERT: A 550 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6961 (mt-10) REVERT: A 624 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7501 (mtm-85) REVERT: B 314 GLN cc_start: 0.5796 (mt0) cc_final: 0.5594 (mm110) outliers start: 14 outliers final: 13 residues processed: 102 average time/residue: 0.4583 time to fit residues: 60.2272 Evaluate side-chains 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.171908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141425 restraints weight = 22607.551| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.17 r_work: 0.3512 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6732 Z= 0.134 Angle : 0.474 4.817 9132 Z= 0.263 Chirality : 0.035 0.133 987 Planarity : 0.004 0.036 1093 Dihedral : 11.245 96.295 1025 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 15.90 % Favored : 81.87 % 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: 2.92 (0.30), residues: 750 helix: 2.87 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 528 HIS 0.009 0.001 HIS A 441 PHE 0.035 0.001 PHE A 487 TYR 0.016 0.001 TYR B 518 ARG 0.004 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 468) hydrogen bonds : angle 3.95897 ( 1404) SS BOND : bond 0.00405 ( 2) SS BOND : angle 1.09883 ( 4) covalent geometry : bond 0.00292 ( 6730) covalent geometry : angle 0.47391 ( 9128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.19 seconds wall clock time: 103 minutes 30.44 seconds (6210.44 seconds total)