Starting phenix.real_space_refine on Wed Jun 11 16:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvl_47210/06_2025/9dvl_47210_trim.cif" } resolution = 2.97 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= 0.032 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 8 5.49 5 S 32 5.16 5 C 4382 2.51 5 N 1008 2.21 5 O 1060 1.98 5 H 6284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12774 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: 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: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.78, per 1000 atoms: 0.61 Number of scatterers: 12774 At special positions: 0 Unit cell: (73.4695, 78.4225, 126.302, 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 8 15.00 O 1060 8.00 N 1008 7.00 C 4382 6.00 H 6284 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: 3.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 81.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.320A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.606A 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 removed outlier: 3.836A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.099A 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 453 removed outlier: 3.655A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 472 through 502 removed outlier: 3.935A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.816A 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: 3.919A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (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 230 through 258 Processing helix chain 'B' and resid 267 through 296 removed outlier: 4.332A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.948A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 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: 4.113A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.013A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 618 removed outlier: 4.742A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix 467 hydrogen bonds defined for protein. 1401 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: 4.27 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6268 1.03 - 1.23: 53 1.23 - 1.43: 2919 1.43 - 1.62: 3696 1.62 - 1.82: 48 Bond restraints: 12984 Sorted by residual: bond pdb=" O3P CPL B 805 " pdb=" P CPL B 805 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3P CPL A 805 " pdb=" P CPL A 805 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O4 PO4 B 802 " pdb=" P PO4 B 802 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O4P CPL B 805 " pdb=" P CPL B 805 " ideal model delta sigma weight residual 1.648 1.713 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O4P CPL A 805 " pdb=" P CPL A 805 " ideal model delta sigma weight residual 1.648 1.713 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 12979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 23185 3.05 - 6.10: 67 6.10 - 9.15: 11 9.15 - 12.19: 3 12.19 - 15.24: 2 Bond angle restraints: 23268 Sorted by residual: angle pdb=" O1P CPL B 805 " pdb=" P CPL B 805 " pdb=" O2P CPL B 805 " 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 A 805 " pdb=" P CPL A 805 " pdb=" O2P CPL A 805 " ideal model delta sigma weight residual 119.55 134.76 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N CPL A 805 " pdb=" C5 CPL A 805 " pdb=" C4 CPL A 805 " ideal model delta sigma weight residual 117.50 107.92 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N CPL B 805 " pdb=" C5 CPL B 805 " pdb=" C4 CPL B 805 " ideal model delta sigma weight residual 117.50 108.04 9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" CB MET B 508 " pdb=" CG MET B 508 " pdb=" SD MET B 508 " ideal model delta sigma weight residual 112.70 121.89 -9.19 3.00e+00 1.11e-01 9.38e+00 ... (remaining 23263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 6013 31.54 - 63.09: 244 63.09 - 94.63: 13 94.63 - 126.18: 4 126.18 - 157.72: 2 Dihedral angle restraints: 6276 sinusoidal: 3276 harmonic: 3000 Sorted by residual: dihedral pdb=" C3 CPL A 805 " pdb=" C1 CPL A 805 " pdb=" C2 CPL A 805 " pdb=" O3P CPL A 805 " ideal model delta sinusoidal sigma weight residual 72.09 -85.63 157.72 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O2 CPL A 805 " pdb=" C1 CPL A 805 " pdb=" C2 CPL A 805 " pdb=" O3P CPL A 805 " ideal model delta sinusoidal sigma weight residual 309.18 153.73 155.45 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C33 CPL B 805 " pdb=" C31 CPL B 805 " pdb=" C32 CPL B 805 " pdb=" O2 CPL B 805 " ideal model delta sinusoidal sigma weight residual 171.65 49.00 122.65 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 900 0.072 - 0.143: 78 0.143 - 0.215: 0 0.215 - 0.286: 2 0.286 - 0.357: 8 Chirality restraints: 988 Sorted by residual: chirality pdb=" C17 CLR B 804 " pdb=" C13 CLR B 804 " pdb=" C16 CLR B 804 " pdb=" C20 CLR B 804 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C17 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C16 CLR A 804 " pdb=" C20 CLR A 804 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C13 CLR A 804 " pdb=" C12 CLR A 804 " pdb=" C14 CLR A 804 " pdb=" C17 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.93 -3.27 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 985 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 565 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" N ASP B 566 " -0.040 2.00e-02 2.50e+03 pdb=" CA ASP B 566 " 0.010 2.00e-02 2.50e+03 pdb=" H ASP B 566 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 496 " 0.013 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" CG TYR A 496 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 496 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 496 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 496 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 496 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 496 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 496 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 496 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 496 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 496 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 496 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 565 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C GLU B 565 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU B 565 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 566 " 0.008 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 893 2.21 - 2.81: 26209 2.81 - 3.40: 38040 3.40 - 4.00: 48100 4.00 - 4.60: 74022 Nonbonded interactions: 187264 Sorted by model distance: nonbonded pdb="HH22 ARG B 270 " pdb=" O3 PO4 B 803 " model vdw 1.610 2.450 nonbonded pdb=" HH TYR B 559 " pdb=" OE2 GLU B 613 " model vdw 1.613 2.450 nonbonded pdb=" OD2 ASP B 529 " pdb=" HE ARG B 570 " model vdw 1.620 2.450 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.626 2.450 nonbonded pdb=" O ILE B 271 " pdb=" HH TYR B 352 " model vdw 1.658 2.450 ... (remaining 187259 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.690 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: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.450 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 0.107 6702 Z= 0.229 Angle : 0.671 15.242 9112 Z= 0.296 Chirality : 0.047 0.357 988 Planarity : 0.003 0.037 1082 Dihedral : 17.605 157.720 2452 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 17.96 % Favored : 81.14 % 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: 3.62 (0.30), residues: 744 helix: 3.45 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 327 HIS 0.005 0.001 HIS A 441 PHE 0.013 0.001 PHE A 610 TYR 0.030 0.001 TYR A 496 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.09493 ( 467) hydrogen bonds : angle 4.65677 ( 1401) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.58588 ( 4) covalent geometry : bond 0.00456 ( 6700) covalent geometry : angle 0.67063 ( 9108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.6862 (p90) REVERT: A 609 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6778 (t80) REVERT: B 591 ILE cc_start: 0.7322 (mm) cc_final: 0.7072 (mt) outliers start: 6 outliers final: 1 residues processed: 85 average time/residue: 1.5931 time to fit residues: 146.5773 Evaluate side-chains 65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.0050 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140789 restraints weight = 18453.081| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.85 r_work: 0.3315 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6702 Z= 0.132 Angle : 0.476 4.439 9112 Z= 0.257 Chirality : 0.035 0.130 988 Planarity : 0.004 0.035 1082 Dihedral : 13.304 145.701 1054 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.80 % Allowed : 16.77 % Favored : 81.44 % 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: 3.46 (0.30), residues: 744 helix: 3.25 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 327 HIS 0.005 0.001 HIS A 441 PHE 0.018 0.001 PHE B 244 TYR 0.017 0.001 TYR A 496 ARG 0.004 0.001 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 467) hydrogen bonds : angle 4.28957 ( 1401) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.10067 ( 4) covalent geometry : bond 0.00280 ( 6700) covalent geometry : angle 0.47562 ( 9108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7039 (m-10) cc_final: 0.6732 (m-10) REVERT: B 386 PHE cc_start: 0.7508 (m-10) cc_final: 0.7213 (m-10) REVERT: B 441 HIS cc_start: 0.5995 (p-80) cc_final: 0.5249 (t-90) REVERT: B 445 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6442 (p90) REVERT: B 468 ARG cc_start: 0.6054 (tmm160) cc_final: 0.5658 (ttm170) REVERT: B 591 ILE cc_start: 0.6952 (mm) cc_final: 0.6679 (mt) REVERT: B 608 ASN cc_start: 0.7832 (m-40) cc_final: 0.7557 (m-40) outliers start: 12 outliers final: 3 residues processed: 77 average time/residue: 1.7055 time to fit residues: 141.9599 Evaluate side-chains 66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 57 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: A 504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124995 restraints weight = 18575.737| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.88 r_work: 0.3100 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6702 Z= 0.160 Angle : 0.520 6.141 9112 Z= 0.282 Chirality : 0.036 0.171 988 Planarity : 0.004 0.052 1082 Dihedral : 11.783 114.133 1052 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.10 % Allowed : 15.57 % Favored : 82.34 % 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: 2.94 (0.30), residues: 744 helix: 2.91 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.86 (0.38), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 395 HIS 0.005 0.001 HIS A 313 PHE 0.032 0.002 PHE B 605 TYR 0.016 0.002 TYR A 272 ARG 0.005 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06169 ( 467) hydrogen bonds : angle 4.25875 ( 1401) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.27346 ( 4) covalent geometry : bond 0.00352 ( 6700) covalent geometry : angle 0.51985 ( 9108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7925 (tttt) cc_final: 0.7383 (mttm) REVERT: A 472 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7238 (mmm160) REVERT: B 301 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7660 (tt) REVERT: B 441 HIS cc_start: 0.6368 (p-80) cc_final: 0.5671 (t-90) REVERT: B 591 ILE cc_start: 0.7287 (mm) cc_final: 0.7003 (mt) outliers start: 14 outliers final: 4 residues processed: 87 average time/residue: 1.7190 time to fit residues: 161.4779 Evaluate side-chains 73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 chunk 12 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125453 restraints weight = 18454.000| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.86 r_work: 0.3104 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6702 Z= 0.119 Angle : 0.460 4.385 9112 Z= 0.251 Chirality : 0.034 0.131 988 Planarity : 0.004 0.047 1082 Dihedral : 11.319 117.731 1050 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.35 % Allowed : 17.22 % Favored : 81.44 % 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: 3.14 (0.30), residues: 744 helix: 2.97 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.003 0.001 HIS B 476 PHE 0.023 0.001 PHE B 605 TYR 0.013 0.001 TYR A 496 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05374 ( 467) hydrogen bonds : angle 4.14188 ( 1401) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.18599 ( 4) covalent geometry : bond 0.00239 ( 6700) covalent geometry : angle 0.45954 ( 9108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7290 (mmm160) REVERT: B 361 ASN cc_start: 0.7694 (t0) cc_final: 0.7325 (t0) REVERT: B 386 PHE cc_start: 0.7703 (m-10) cc_final: 0.7488 (m-10) REVERT: B 441 HIS cc_start: 0.6434 (p-80) cc_final: 0.5741 (t-90) REVERT: B 591 ILE cc_start: 0.7234 (mm) cc_final: 0.6966 (mt) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 1.7028 time to fit residues: 147.2802 Evaluate side-chains 75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119463 restraints weight = 18708.224| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.93 r_work: 0.3125 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6702 Z= 0.140 Angle : 0.472 4.388 9112 Z= 0.257 Chirality : 0.035 0.157 988 Planarity : 0.004 0.046 1082 Dihedral : 10.921 111.737 1050 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.65 % Allowed : 16.32 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.30), residues: 744 helix: 2.89 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 573 HIS 0.004 0.001 HIS B 476 PHE 0.024 0.001 PHE B 605 TYR 0.012 0.001 TYR A 272 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05644 ( 467) hydrogen bonds : angle 4.11512 ( 1401) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.24271 ( 4) covalent geometry : bond 0.00306 ( 6700) covalent geometry : angle 0.47125 ( 9108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7276 (mmm160) REVERT: B 441 HIS cc_start: 0.6560 (p-80) cc_final: 0.5923 (t-90) REVERT: B 591 ILE cc_start: 0.7256 (mm) cc_final: 0.6969 (mt) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 1.7655 time to fit residues: 152.3381 Evaluate side-chains 71 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 618 ASN B 248 ASN B 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115870 restraints weight = 19022.942| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.95 r_work: 0.3005 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6702 Z= 0.162 Angle : 0.493 4.503 9112 Z= 0.271 Chirality : 0.036 0.163 988 Planarity : 0.004 0.048 1082 Dihedral : 10.867 108.676 1050 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.25 % Allowed : 16.02 % Favored : 81.74 % 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: 2.80 (0.30), residues: 744 helix: 2.74 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 573 HIS 0.005 0.001 HIS B 476 PHE 0.027 0.002 PHE B 605 TYR 0.018 0.002 TYR A 496 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 467) hydrogen bonds : angle 4.19498 ( 1401) SS BOND : bond 0.00436 ( 2) SS BOND : angle 1.36232 ( 4) covalent geometry : bond 0.00360 ( 6700) covalent geometry : angle 0.49203 ( 9108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7957 (tttt) cc_final: 0.7422 (mttm) REVERT: A 472 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7380 (mmm160) REVERT: A 575 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7280 (mt) REVERT: B 441 HIS cc_start: 0.6648 (p-80) cc_final: 0.6047 (t-90) REVERT: B 591 ILE cc_start: 0.7404 (mm) cc_final: 0.7114 (mt) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 1.5530 time to fit residues: 139.6868 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 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 576 GLN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116910 restraints weight = 18683.556| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.92 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6702 Z= 0.139 Angle : 0.474 4.780 9112 Z= 0.260 Chirality : 0.035 0.132 988 Planarity : 0.004 0.047 1082 Dihedral : 10.673 106.949 1050 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.80 % Allowed : 16.77 % Favored : 81.44 % 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: 2.84 (0.30), residues: 744 helix: 2.77 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 573 HIS 0.004 0.001 HIS B 476 PHE 0.024 0.002 PHE B 605 TYR 0.010 0.001 TYR A 272 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05784 ( 467) hydrogen bonds : angle 4.16110 ( 1401) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.32390 ( 4) covalent geometry : bond 0.00300 ( 6700) covalent geometry : angle 0.47315 ( 9108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7977 (tttt) cc_final: 0.7477 (mttm) REVERT: A 575 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7262 (mt) REVERT: B 441 HIS cc_start: 0.6668 (p-80) cc_final: 0.6021 (t-90) REVERT: B 505 SER cc_start: 0.6634 (OUTLIER) cc_final: 0.6286 (t) REVERT: B 591 ILE cc_start: 0.7470 (mm) cc_final: 0.7164 (mt) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 1.6705 time to fit residues: 146.3751 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE 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 B residue 505 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113505 restraints weight = 18902.049| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.95 r_work: 0.3008 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6702 Z= 0.194 Angle : 0.528 4.868 9112 Z= 0.291 Chirality : 0.037 0.136 988 Planarity : 0.004 0.051 1082 Dihedral : 10.741 102.861 1050 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 16.17 % Favored : 81.59 % 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 (0.30), residues: 744 helix: 2.51 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.10 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 573 HIS 0.006 0.001 HIS B 476 PHE 0.031 0.002 PHE B 605 TYR 0.024 0.002 TYR A 496 ARG 0.004 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06745 ( 467) hydrogen bonds : angle 4.30214 ( 1401) SS BOND : bond 0.00497 ( 2) SS BOND : angle 1.43613 ( 4) covalent geometry : bond 0.00447 ( 6700) covalent geometry : angle 0.52715 ( 9108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7938 (tttt) cc_final: 0.7410 (mttm) REVERT: A 575 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7305 (mt) REVERT: B 441 HIS cc_start: 0.6754 (p-80) cc_final: 0.6546 (p-80) REVERT: B 505 SER cc_start: 0.6997 (OUTLIER) cc_final: 0.6651 (t) REVERT: B 591 ILE cc_start: 0.7491 (mm) cc_final: 0.7191 (mt) outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.9269 time to fit residues: 170.6844 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE 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 B residue 335 PHE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 576 GLN B 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116828 restraints weight = 18794.035| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.93 r_work: 0.3026 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6702 Z= 0.121 Angle : 0.465 4.611 9112 Z= 0.257 Chirality : 0.035 0.131 988 Planarity : 0.004 0.044 1082 Dihedral : 10.292 103.331 1050 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.65 % Allowed : 17.37 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.30), residues: 744 helix: 2.76 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.94 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS B 476 PHE 0.021 0.001 PHE B 605 TYR 0.017 0.001 TYR A 345 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 467) hydrogen bonds : angle 4.16005 ( 1401) SS BOND : bond 0.00367 ( 2) SS BOND : angle 1.34057 ( 4) covalent geometry : bond 0.00244 ( 6700) covalent geometry : angle 0.46447 ( 9108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7945 (tttt) cc_final: 0.7422 (mttm) REVERT: A 496 TYR cc_start: 0.7734 (t80) cc_final: 0.7455 (t80) REVERT: A 575 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7234 (mt) REVERT: B 505 SER cc_start: 0.6957 (OUTLIER) cc_final: 0.6602 (t) REVERT: B 591 ILE cc_start: 0.7475 (mm) cc_final: 0.7176 (mt) outliers start: 11 outliers final: 5 residues processed: 82 average time/residue: 1.6568 time to fit residues: 146.8980 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE 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 B residue 505 SER Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 248 ASN B 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118588 restraints weight = 18682.806| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.89 r_work: 0.3025 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6702 Z= 0.159 Angle : 0.497 5.543 9112 Z= 0.272 Chirality : 0.036 0.146 988 Planarity : 0.004 0.043 1082 Dihedral : 10.290 100.155 1050 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.50 % Allowed : 17.66 % Favored : 80.84 % 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: 2.71 (0.30), residues: 744 helix: 2.66 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.00 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.009 0.001 HIS B 441 PHE 0.027 0.002 PHE B 605 TYR 0.014 0.002 TYR A 272 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06107 ( 467) hydrogen bonds : angle 4.20560 ( 1401) SS BOND : bond 0.00426 ( 2) SS BOND : angle 1.34011 ( 4) covalent geometry : bond 0.00355 ( 6700) covalent geometry : angle 0.49658 ( 9108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7956 (tttt) cc_final: 0.7443 (mttm) REVERT: A 575 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 505 SER cc_start: 0.7092 (OUTLIER) cc_final: 0.6745 (t) REVERT: B 591 ILE cc_start: 0.7511 (mm) cc_final: 0.7202 (mt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 1.7285 time to fit residues: 143.4306 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 PHE 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 B residue 335 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 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 576 GLN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117247 restraints weight = 18648.258| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.86 r_work: 0.3015 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6702 Z= 0.139 Angle : 0.481 5.179 9112 Z= 0.263 Chirality : 0.035 0.134 988 Planarity : 0.004 0.051 1082 Dihedral : 10.171 99.291 1050 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.80 % Allowed : 17.37 % Favored : 80.84 % 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: 2.77 (0.30), residues: 744 helix: 2.71 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.00 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.008 0.001 HIS B 441 PHE 0.024 0.001 PHE B 605 TYR 0.014 0.001 TYR A 345 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05829 ( 467) hydrogen bonds : angle 4.17407 ( 1401) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.35165 ( 4) covalent geometry : bond 0.00299 ( 6700) covalent geometry : angle 0.48008 ( 9108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8705.22 seconds wall clock time: 151 minutes 11.02 seconds (9071.02 seconds total)