Starting phenix.real_space_refine on Thu Sep 18 01:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvl_47210/09_2025/9dvl_47210_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvl_47210/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dvl_47210/09_2025/9dvl_47210_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvl_47210/09_2025/9dvl_47210_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvl_47210/09_2025/9dvl_47210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvl_47210/09_2025/9dvl_47210.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.19 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: 1.20 Conformation dependent library (CDL) restraints added in 407.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.28 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: 2.73 Time building geometry restraints manager: 1.64 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: 5.610 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 270 TYR 0.030 0.001 TYR A 496 PHE 0.013 0.001 PHE A 610 TRP 0.008 0.001 TRP B 327 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6700) covalent geometry : angle 0.67063 ( 9108) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.58588 ( 4) hydrogen bonds : bond 0.09493 ( 467) hydrogen bonds : angle 4.65677 ( 1401) *********************** 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 : 0.315 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: 0.7071 (mt) outliers start: 6 outliers final: 1 residues processed: 85 average time/residue: 0.8442 time to fit residues: 77.1665 Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.161396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123981 restraints weight = 18694.281| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.94 r_work: 0.3130 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6702 Z= 0.203 Angle : 0.556 4.590 9112 Z= 0.302 Chirality : 0.038 0.132 988 Planarity : 0.005 0.064 1082 Dihedral : 13.333 141.129 1054 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.80 % Allowed : 16.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.30), residues: 744 helix: 2.93 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 604 TYR 0.021 0.002 TYR A 496 PHE 0.030 0.002 PHE B 605 TRP 0.011 0.002 TRP A 395 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6700) covalent geometry : angle 0.55549 ( 9108) SS BOND : bond 0.00486 ( 2) SS BOND : angle 1.43872 ( 4) hydrogen bonds : bond 0.06040 ( 467) hydrogen bonds : angle 4.43806 ( 1401) *********************** 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 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 472 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6990 (mmm160) REVERT: B 386 PHE cc_start: 0.7628 (m-10) cc_final: 0.7400 (m-10) REVERT: B 445 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6624 (p90) REVERT: B 591 ILE cc_start: 0.7028 (mm) cc_final: 0.6781 (mt) outliers start: 12 outliers final: 3 residues processed: 79 average time/residue: 0.9620 time to fit residues: 81.3531 Evaluate side-chains 68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 445 TYR Chi-restraints excluded: chain B residue 565 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 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 B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122195 restraints weight = 18845.362| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2130 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= 0.155 Angle : 0.497 4.215 9112 Z= 0.270 Chirality : 0.035 0.132 988 Planarity : 0.004 0.053 1082 Dihedral : 11.703 111.931 1050 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.10 % Allowed : 16.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.30), residues: 744 helix: 2.78 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 448 TYR 0.009 0.001 TYR B 352 PHE 0.026 0.002 PHE B 605 TRP 0.009 0.001 TRP A 573 HIS 0.010 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6700) covalent geometry : angle 0.49577 ( 9108) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.40594 ( 4) hydrogen bonds : bond 0.05976 ( 467) hydrogen bonds : angle 4.23750 ( 1401) *********************** 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 86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7277 (mmm160) REVERT: B 386 PHE cc_start: 0.7721 (m-10) cc_final: 0.7508 (m-10) REVERT: B 591 ILE cc_start: 0.7285 (mm) cc_final: 0.7007 (mt) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 0.9051 time to fit residues: 82.5235 Evaluate side-chains 72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 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 = 0.3664 r_free = 0.3664 target = 0.150086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112454 restraints weight = 18989.800| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.94 r_work: 0.2979 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6702 Z= 0.206 Angle : 0.538 4.385 9112 Z= 0.297 Chirality : 0.038 0.135 988 Planarity : 0.004 0.054 1082 Dihedral : 11.289 112.866 1050 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.25 % Allowed : 15.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.30), residues: 744 helix: 2.51 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.10 (0.40), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 604 TYR 0.023 0.002 TYR A 496 PHE 0.032 0.002 PHE B 605 TRP 0.010 0.002 TRP A 573 HIS 0.006 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6700) covalent geometry : angle 0.53689 ( 9108) SS BOND : bond 0.00537 ( 2) SS BOND : angle 1.68178 ( 4) hydrogen bonds : bond 0.06806 ( 467) hydrogen bonds : angle 4.36158 ( 1401) *********************** 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: 15 poor density : 68 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7969 (tttt) cc_final: 0.7416 (mttm) REVERT: A 472 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7469 (mmm160) REVERT: B 445 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.7074 (p90) REVERT: B 591 ILE cc_start: 0.7481 (mm) cc_final: 0.7195 (mt) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.9113 time to fit residues: 79.4347 Evaluate side-chains 75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 B residue 335 PHE Chi-restraints excluded: chain B residue 445 TYR 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 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116511 restraints weight = 18720.350| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.94 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6702 Z= 0.138 Angle : 0.484 4.731 9112 Z= 0.272 Chirality : 0.036 0.297 988 Planarity : 0.004 0.051 1082 Dihedral : 10.977 109.379 1050 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.40 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.30), residues: 744 helix: 2.66 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.099 0.002 TYR A 496 PHE 0.024 0.001 PHE B 605 TRP 0.009 0.001 TRP A 573 HIS 0.006 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6700) covalent geometry : angle 0.48354 ( 9108) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.47937 ( 4) hydrogen bonds : bond 0.05992 ( 467) hydrogen bonds : angle 4.25837 ( 1401) *********************** 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: 16 poor density : 69 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7939 (tttt) cc_final: 0.7426 (mttm) REVERT: A 472 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7381 (mmm160) REVERT: A 575 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7141 (mt) REVERT: B 591 ILE cc_start: 0.7414 (mm) cc_final: 0.7138 (mt) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.9609 time to fit residues: 85.2833 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 : 0.340 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.151494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114731 restraints weight = 18742.870| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.91 r_work: 0.2961 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6702 Z= 0.200 Angle : 0.538 6.525 9112 Z= 0.299 Chirality : 0.038 0.174 988 Planarity : 0.004 0.054 1082 Dihedral : 11.092 106.111 1050 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 15.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.30), residues: 744 helix: 2.41 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.14 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 604 TYR 0.077 0.002 TYR A 496 PHE 0.031 0.002 PHE B 605 TRP 0.010 0.001 TRP A 573 HIS 0.006 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6700) covalent geometry : angle 0.53730 ( 9108) SS BOND : bond 0.00548 ( 2) SS BOND : angle 1.61796 ( 4) hydrogen bonds : bond 0.06899 ( 467) hydrogen bonds : angle 4.35324 ( 1401) *********************** 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 79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7986 (tttt) cc_final: 0.7473 (mttm) REVERT: A 472 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7547 (mtm110) REVERT: A 575 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7268 (mt) REVERT: B 591 ILE cc_start: 0.7440 (mm) cc_final: 0.7144 (mt) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 1.0575 time to fit residues: 86.7146 Evaluate side-chains 72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 335 PHE 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 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.154341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117913 restraints weight = 18625.281| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.91 r_work: 0.2971 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6702 Z= 0.159 Angle : 0.502 7.724 9112 Z= 0.280 Chirality : 0.036 0.196 988 Planarity : 0.004 0.050 1082 Dihedral : 10.931 105.425 1050 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 15.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.30), residues: 744 helix: 2.47 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.074 0.002 TYR A 496 PHE 0.025 0.002 PHE B 605 TRP 0.010 0.001 TRP A 573 HIS 0.006 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6700) covalent geometry : angle 0.50076 ( 9108) SS BOND : bond 0.00459 ( 2) SS BOND : angle 1.54999 ( 4) hydrogen bonds : bond 0.06341 ( 467) hydrogen bonds : angle 4.29535 ( 1401) *********************** 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: 15 poor density : 68 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7961 (tttt) cc_final: 0.7451 (mttm) REVERT: A 472 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7608 (mtp85) REVERT: A 575 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7205 (mt) REVERT: B 591 ILE cc_start: 0.7500 (mm) cc_final: 0.7201 (mt) outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 0.9405 time to fit residues: 82.7694 Evaluate side-chains 72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 overall best weight: 0.6202 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.151023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113970 restraints weight = 18511.120| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.92 r_work: 0.2963 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6702 Z= 0.154 Angle : 0.505 8.664 9112 Z= 0.278 Chirality : 0.036 0.158 988 Planarity : 0.004 0.046 1082 Dihedral : 10.707 103.968 1050 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.80 % Allowed : 16.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.30), residues: 744 helix: 2.53 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.06 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 604 TYR 0.061 0.002 TYR A 496 PHE 0.025 0.002 PHE B 605 TRP 0.009 0.001 TRP B 514 HIS 0.006 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6700) covalent geometry : angle 0.50428 ( 9108) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.48095 ( 4) hydrogen bonds : bond 0.06145 ( 467) hydrogen bonds : angle 4.25644 ( 1401) *********************** 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 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7965 (tttt) cc_final: 0.7462 (mttm) REVERT: A 472 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7634 (mtp85) REVERT: A 575 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7182 (mt) REVERT: B 591 ILE cc_start: 0.7488 (mm) cc_final: 0.7182 (mt) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.9861 time to fit residues: 81.3587 Evaluate side-chains 75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 335 PHE 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 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.152337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115256 restraints weight = 18726.548| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.93 r_work: 0.2992 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6702 Z= 0.137 Angle : 0.482 9.499 9112 Z= 0.267 Chirality : 0.035 0.134 988 Planarity : 0.004 0.040 1082 Dihedral : 10.417 101.569 1050 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.80 % Allowed : 16.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.30), residues: 744 helix: 2.66 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.98 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.039 0.002 TYR A 496 PHE 0.022 0.001 PHE B 605 TRP 0.010 0.001 TRP A 573 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6700) covalent geometry : angle 0.48074 ( 9108) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.47848 ( 4) hydrogen bonds : bond 0.05750 ( 467) hydrogen bonds : angle 4.18349 ( 1401) *********************** 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 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7970 (tttt) cc_final: 0.7476 (mttm) REVERT: A 472 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7565 (mtp85) REVERT: A 575 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7187 (mt) REVERT: B 394 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8431 (t80) REVERT: B 591 ILE cc_start: 0.7492 (mm) cc_final: 0.7176 (mt) outliers start: 12 outliers final: 5 residues processed: 79 average time/residue: 1.0182 time to fit residues: 86.0239 Evaluate side-chains 73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 394 PHE 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 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.151512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114993 restraints weight = 18743.464| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.92 r_work: 0.2959 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3370 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 : 0.488 5.534 9112 Z= 0.269 Chirality : 0.036 0.161 988 Planarity : 0.004 0.049 1082 Dihedral : 10.443 102.869 1050 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.30), residues: 744 helix: 2.60 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -2.00 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 604 TYR 0.017 0.002 TYR A 496 PHE 0.026 0.002 PHE B 605 TRP 0.009 0.001 TRP B 514 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6700) covalent geometry : angle 0.48727 ( 9108) SS BOND : bond 0.00460 ( 2) SS BOND : angle 1.47823 ( 4) hydrogen bonds : bond 0.06035 ( 467) hydrogen bonds : angle 4.21842 ( 1401) ********************** 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 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7965 (tttt) cc_final: 0.7470 (mttm) REVERT: A 472 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7555 (mtm110) REVERT: A 575 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7213 (mt) REVERT: B 394 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8484 (t80) REVERT: B 591 ILE cc_start: 0.7479 (mm) cc_final: 0.7159 (mt) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 1.0080 time to fit residues: 81.8370 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 : 0.355 ------------------------------------------------------------------------------- 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 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 394 PHE 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 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 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 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 = 0.3715 r_free = 0.3715 target = 0.153224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117241 restraints weight = 18773.277| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.90 r_work: 0.2947 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3439 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= 0.162 Angle : 0.494 5.271 9112 Z= 0.273 Chirality : 0.036 0.135 988 Planarity : 0.004 0.046 1082 Dihedral : 10.491 104.149 1050 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.30), residues: 744 helix: 2.56 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.021 0.002 TYR A 496 PHE 0.027 0.002 PHE B 605 TRP 0.011 0.001 TRP A 573 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6700) covalent geometry : angle 0.49295 ( 9108) SS BOND : bond 0.00463 ( 2) SS BOND : angle 1.51502 ( 4) hydrogen bonds : bond 0.06239 ( 467) hydrogen bonds : angle 4.24860 ( 1401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.56 seconds wall clock time: 74 minutes 53.58 seconds (4493.58 seconds total)