Starting phenix.real_space_refine on Thu May 15 09:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvl_47210/05_2025/9dvl_47210_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvl_47210/05_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_47210/05_2025/9dvl_47210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvl_47210/05_2025/9dvl_47210.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvl_47210/05_2025/9dvl_47210_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvl_47210/05_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-5687/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: 7.25, per 1000 atoms: 0.57 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: 3.48 Conformation dependent library (CDL) restraints added in 842.4 milliseconds 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: 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: 4.320A 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: 4.33 Time building geometry restraints manager: 4.14 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: 0.01 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: 2.860 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: 0.100 Set scattering table: 0.140 Process input model: 30.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- 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 : 0.899 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: 1.6181 time to fit residues: 149.0702 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 : 0.926 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140830 restraints weight = 18453.042| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.84 r_work: 0.3316 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 4.440 9112 Z= 0.257 Chirality : 0.035 0.130 988 Planarity : 0.004 0.035 1082 Dihedral : 13.304 145.700 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 4.28955 ( 1401) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.10069 ( 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 : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.7030 (m-10) cc_final: 0.6727 (m-10) REVERT: B 386 PHE cc_start: 0.7497 (m-10) cc_final: 0.7206 (m-10) REVERT: B 441 HIS cc_start: 0.5987 (p-80) cc_final: 0.5242 (t-90) REVERT: B 445 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6424 (p90) REVERT: B 468 ARG cc_start: 0.6033 (tmm160) cc_final: 0.5639 (ttm170) REVERT: B 591 ILE cc_start: 0.6933 (mm) cc_final: 0.6660 (mt) REVERT: B 608 ASN cc_start: 0.7816 (m-40) cc_final: 0.7541 (m-40) outliers start: 12 outliers final: 3 residues processed: 77 average time/residue: 1.6904 time to fit residues: 140.5936 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 : 0.902 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 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: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118005 restraints weight = 18728.719| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.88 r_work: 0.3031 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6702 Z= 0.196 Angle : 0.572 6.927 9112 Z= 0.311 Chirality : 0.038 0.179 988 Planarity : 0.005 0.061 1082 Dihedral : 11.930 112.813 1052 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.40 % Allowed : 15.42 % Favored : 82.19 % 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: 2.59 (0.30), residues: 744 helix: 2.57 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 395 HIS 0.007 0.002 HIS A 499 PHE 0.040 0.002 PHE B 605 TYR 0.021 0.002 TYR A 272 ARG 0.005 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.06954 ( 467) hydrogen bonds : angle 4.41636 ( 1401) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.42551 ( 4) covalent geometry : bond 0.00435 ( 6700) covalent geometry : angle 0.57141 ( 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 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7924 (tttt) cc_final: 0.7381 (mttm) REVERT: A 472 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7303 (mmm160) REVERT: B 441 HIS cc_start: 0.6451 (p-80) cc_final: 0.5810 (t-90) REVERT: B 591 ILE cc_start: 0.7326 (mm) cc_final: 0.7042 (mt) outliers start: 16 outliers final: 5 residues processed: 83 average time/residue: 1.7638 time to fit residues: 157.3885 Evaluate side-chains 67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 471 LYS 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: 0.0870 chunk 18 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.158894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123149 restraints weight = 18546.525| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.83 r_work: 0.3098 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 6702 Z= 0.127 Angle : 0.466 4.320 9112 Z= 0.257 Chirality : 0.035 0.132 988 Planarity : 0.004 0.050 1082 Dihedral : 11.339 116.840 1050 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.95 % Allowed : 16.32 % 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: 2.89 (0.30), residues: 744 helix: 2.80 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 573 HIS 0.004 0.001 HIS A 441 PHE 0.024 0.001 PHE B 605 TYR 0.014 0.001 TYR A 496 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 467) hydrogen bonds : angle 4.20457 ( 1401) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.31767 ( 4) covalent geometry : bond 0.00257 ( 6700) covalent geometry : angle 0.46576 ( 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 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8311 (mmtp) REVERT: A 472 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7320 (mmm160) REVERT: B 441 HIS cc_start: 0.6549 (p-80) cc_final: 0.5863 (t-90) REVERT: B 591 ILE cc_start: 0.7310 (mm) cc_final: 0.7044 (mt) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 1.7250 time to fit residues: 152.4401 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 471 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain B residue 278 LEU 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=3.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116483 restraints weight = 18787.268| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.93 r_work: 0.3100 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2624 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= 0.143 Angle : 0.481 4.349 9112 Z= 0.263 Chirality : 0.035 0.133 988 Planarity : 0.004 0.048 1082 Dihedral : 10.850 110.386 1050 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.10 % Allowed : 16.02 % Favored : 81.89 % 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 : -2.00 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 573 HIS 0.004 0.001 HIS B 476 PHE 0.025 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 0.05854 ( 467) hydrogen bonds : angle 4.17341 ( 1401) SS BOND : bond 0.00396 ( 2) SS BOND : angle 1.35087 ( 4) covalent geometry : bond 0.00312 ( 6700) covalent geometry : angle 0.48032 ( 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 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7938 (tttt) cc_final: 0.7409 (mttm) REVERT: A 575 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 441 HIS cc_start: 0.6588 (p-80) cc_final: 0.5925 (t-90) REVERT: B 591 ILE cc_start: 0.7322 (mm) cc_final: 0.7042 (mt) outliers start: 14 outliers final: 7 residues processed: 83 average time/residue: 1.6409 time to fit residues: 147.5665 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 278 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 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 B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.155856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119634 restraints weight = 18934.315| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.90 r_work: 0.3069 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2957 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= 0.164 Angle : 0.498 4.591 9112 Z= 0.274 Chirality : 0.036 0.171 988 Planarity : 0.004 0.048 1082 Dihedral : 10.767 107.886 1050 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 16.47 % 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: 2.65 (0.30), residues: 744 helix: 2.63 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.06 (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 0.022 0.002 TYR A 496 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06211 ( 467) hydrogen bonds : angle 4.23530 ( 1401) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.42040 ( 4) covalent geometry : bond 0.00365 ( 6700) covalent geometry : angle 0.49691 ( 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 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7947 (tttt) cc_final: 0.7438 (mttm) REVERT: A 575 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7291 (mt) REVERT: B 441 HIS cc_start: 0.6680 (p-80) cc_final: 0.6064 (t-90) REVERT: B 591 ILE cc_start: 0.7488 (mm) cc_final: 0.7195 (mt) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 1.5957 time to fit residues: 138.3659 Evaluate side-chains 73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 278 LEU 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: 0.0980 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 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 = 0.3736 r_free = 0.3736 target = 0.155967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120326 restraints weight = 18615.128| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.83 r_work: 0.3081 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2942 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 : 0.461 4.664 9112 Z= 0.252 Chirality : 0.035 0.132 988 Planarity : 0.003 0.042 1082 Dihedral : 10.450 106.096 1050 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.80 % Allowed : 17.22 % 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: 2.92 (0.30), residues: 744 helix: 2.82 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 573 HIS 0.004 0.001 HIS B 476 PHE 0.020 0.001 PHE B 605 TYR 0.018 0.001 TYR A 345 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 467) hydrogen bonds : angle 4.12572 ( 1401) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.31916 ( 4) covalent geometry : bond 0.00247 ( 6700) covalent geometry : angle 0.46005 ( 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 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7267 (mt) REVERT: B 361 ASN cc_start: 0.7788 (t0) cc_final: 0.7429 (t0) REVERT: B 441 HIS cc_start: 0.6671 (p-80) cc_final: 0.6027 (t-90) REVERT: B 591 ILE cc_start: 0.7485 (mm) cc_final: 0.7178 (mt) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 1.5345 time to fit residues: 136.5239 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 : 0.989 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain B residue 335 PHE 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: 0.9990 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: 0.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116359 restraints weight = 18873.857| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.87 r_work: 0.3001 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6702 Z= 0.170 Angle : 0.503 5.474 9112 Z= 0.275 Chirality : 0.036 0.156 988 Planarity : 0.004 0.045 1082 Dihedral : 10.490 103.319 1050 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.54 % Allowed : 16.17 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.30), residues: 744 helix: 2.66 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.05 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 573 HIS 0.006 0.001 HIS B 476 PHE 0.028 0.002 PHE B 605 TYR 0.020 0.002 TYR A 496 ARG 0.005 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.06218 ( 467) hydrogen bonds : angle 4.21087 ( 1401) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.34201 ( 4) covalent geometry : bond 0.00387 ( 6700) covalent geometry : angle 0.50188 ( 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: 17 poor density : 68 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7976 (tttt) cc_final: 0.7461 (mttm) REVERT: A 575 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (mt) REVERT: B 394 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8455 (t80) REVERT: B 441 HIS cc_start: 0.6718 (p-80) cc_final: 0.6101 (t-90) REVERT: B 445 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7085 (p90) REVERT: B 591 ILE cc_start: 0.7531 (mm) cc_final: 0.7228 (mt) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 1.7064 time to fit residues: 149.1727 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 496 TYR 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 278 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 471 LYS 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: 1.9990 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 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 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 = 0.3724 r_free = 0.3724 target = 0.154918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118173 restraints weight = 18819.097| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.93 r_work: 0.3026 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6702 Z= 0.136 Angle : 0.493 5.747 9112 Z= 0.277 Chirality : 0.037 0.334 988 Planarity : 0.004 0.042 1082 Dihedral : 10.293 102.932 1050 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 16.92 % 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: 2.76 (0.30), residues: 744 helix: 2.70 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.96 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.006 0.001 HIS A 499 PHE 0.028 0.001 PHE A 511 TYR 0.078 0.002 TYR A 496 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05785 ( 467) hydrogen bonds : angle 4.21883 ( 1401) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.26752 ( 4) covalent geometry : bond 0.00282 ( 6700) covalent geometry : angle 0.49272 ( 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 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7283 (mt) REVERT: B 441 HIS cc_start: 0.6668 (p-80) cc_final: 0.6035 (t-90) REVERT: B 445 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.7063 (p90) REVERT: B 591 ILE cc_start: 0.7488 (mm) cc_final: 0.7187 (mt) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 1.6523 time to fit residues: 147.8375 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain B residue 445 TYR 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 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116134 restraints weight = 18782.245| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.91 r_work: 0.3015 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6702 Z= 0.152 Angle : 0.490 5.195 9112 Z= 0.267 Chirality : 0.036 0.135 988 Planarity : 0.004 0.041 1082 Dihedral : 10.213 100.682 1050 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 2.68 (0.30), residues: 744 helix: 2.65 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.005 0.001 HIS B 476 PHE 0.025 0.002 PHE B 605 TYR 0.013 0.002 TYR A 272 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 467) hydrogen bonds : angle 4.17637 ( 1401) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.35598 ( 4) covalent geometry : bond 0.00338 ( 6700) covalent geometry : angle 0.48934 ( 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 81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7957 (tttt) cc_final: 0.7457 (mttm) REVERT: A 575 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 441 HIS cc_start: 0.6713 (p-80) cc_final: 0.6483 (p-80) REVERT: B 445 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.7076 (p90) REVERT: B 591 ILE cc_start: 0.7490 (mm) cc_final: 0.7186 (mt) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 1.7801 time to fit residues: 153.4525 Evaluate side-chains 79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 445 TYR 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: 0.9980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.2986 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118102 restraints weight = 18669.623| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.91 r_work: 0.3057 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6702 Z= 0.116 Angle : 0.455 5.034 9112 Z= 0.249 Chirality : 0.035 0.132 988 Planarity : 0.004 0.050 1082 Dihedral : 9.939 99.539 1050 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.65 % Allowed : 17.66 % Favored : 80.69 % 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: 2.98 (0.30), residues: 744 helix: 2.86 (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 0.009 0.001 TRP B 514 HIS 0.003 0.001 HIS B 476 PHE 0.019 0.001 PHE B 605 TYR 0.012 0.001 TYR A 345 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 467) hydrogen bonds : angle 4.08365 ( 1401) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.27619 ( 4) covalent geometry : bond 0.00231 ( 6700) covalent geometry : angle 0.45433 ( 9108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7860.73 seconds wall clock time: 135 minutes 19.15 seconds (8119.15 seconds total)