Starting phenix.real_space_refine on Tue Jul 29 21:27:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.map" model { file = "/net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unl_26626/07_2025/7unl_26626.cif" } resolution = 2.45 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= 0.035 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 K 8 8.98 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1086 1.98 5 H 5900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11724 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Time building chain proxies: 7.42, per 1000 atoms: 0.63 Number of scatterers: 11724 At special positions: 0 Unit cell: (104.55, 70.55, 78.2, 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) K 8 19.00 S 38 16.00 O 1086 8.00 N 938 7.00 C 3754 6.00 H 5900 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.42 Conformation dependent library (CDL) restraints added in 924.8 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.037A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.565A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.711A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.932A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.522A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 removed outlier: 4.520A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.036A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.566A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.710A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.932A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.523A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 461 removed outlier: 4.521A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 466 hydrogen bonds defined for protein. 1368 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: 4.30 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5882 1.03 - 1.22: 18 1.22 - 1.42: 2382 1.42 - 1.61: 3390 1.61 - 1.81: 58 Bond restraints: 11730 Sorted by residual: bond pdb=" CD1 PHE B 314 " pdb=" HD1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.965 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" NE2 GLN A 34 " pdb="HE21 GLN A 34 " ideal model delta sigma weight residual 0.860 0.831 0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" CE1 PHE B 314 " pdb=" HE1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.904 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 11725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 19828 1.14 - 2.27: 1356 2.27 - 3.41: 47 3.41 - 4.54: 29 4.54 - 5.68: 4 Bond angle restraints: 21264 Sorted by residual: angle pdb=" CA GLN A 34 " pdb=" CB GLN A 34 " pdb=" CG GLN A 34 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.06e+00 angle pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.02e+00 angle pdb=" N PHE A 314 " pdb=" CA PHE A 314 " pdb=" CB PHE A 314 " ideal model delta sigma weight residual 109.72 105.67 4.05 1.70e+00 3.46e-01 5.67e+00 angle pdb=" N PHE B 314 " pdb=" CA PHE B 314 " pdb=" CB PHE B 314 " ideal model delta sigma weight residual 109.72 105.76 3.96 1.70e+00 3.46e-01 5.44e+00 angle pdb=" C GLN B 34 " pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " ideal model delta sigma weight residual 110.88 114.45 -3.57 1.57e+00 4.06e-01 5.17e+00 ... (remaining 21259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4995 17.53 - 35.05: 365 35.05 - 52.58: 128 52.58 - 70.11: 32 70.11 - 87.63: 4 Dihedral angle restraints: 5524 sinusoidal: 2932 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 581 0.026 - 0.051: 242 0.051 - 0.077: 94 0.077 - 0.103: 48 0.103 - 0.129: 13 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 314 " 0.026 2.00e-02 2.50e+03 2.83e-02 2.41e+01 pdb=" CG PHE A 314 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 314 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE A 314 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 314 " -0.036 2.00e-02 2.50e+03 pdb=" CZ PHE A 314 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 314 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 314 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 314 " 0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 314 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 314 " 0.000 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" CG PHE B 314 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 314 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 314 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 314 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 314 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 314 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 133 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 134 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " -0.022 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.19: 570 2.19 - 2.92: 30654 2.92 - 3.66: 44464 3.66 - 4.40: 68468 4.40 - 5.14: 107342 Nonbonded interactions: 251498 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.448 2.450 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.449 2.450 nonbonded pdb=" HG SER A 45 " pdb=" O HOH A 802 " model vdw 1.657 2.450 nonbonded pdb=" HG SER B 45 " pdb=" O HOH B 802 " model vdw 1.659 2.450 nonbonded pdb=" O PHE A 434 " pdb=" HG1 THR A 437 " model vdw 1.660 2.450 ... (remaining 251493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 703)) 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: 4.430 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: 0.210 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.290 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.003 0.036 5830 Z= 0.157 Angle : 0.559 5.676 7946 Z= 0.319 Chirality : 0.037 0.129 978 Planarity : 0.004 0.039 974 Dihedral : 14.663 87.635 2034 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % 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: 2.30 (0.34), residues: 726 helix: 1.58 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 1.68 (0.72), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 394 HIS 0.005 0.001 HIS B 328 PHE 0.054 0.002 PHE A 314 TYR 0.011 0.002 TYR A 81 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.12518 ( 466) hydrogen bonds : angle 5.59831 ( 1368) covalent geometry : bond 0.00343 ( 5830) covalent geometry : angle 0.55894 ( 7946) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 99 average time/residue: 2.2221 time to fit residues: 232.1117 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 145 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.069575 restraints weight = 22625.707| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.26 r_work: 0.2670 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.186 Angle : 0.547 4.834 7946 Z= 0.292 Chirality : 0.037 0.129 978 Planarity : 0.004 0.032 974 Dihedral : 4.605 33.988 782 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.46 % Allowed : 13.11 % Favored : 85.44 % 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: 3.48 (0.33), residues: 726 helix: 2.42 (0.21), residues: 606 sheet: None (None), residues: 0 loop : 1.89 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.001 PHE A 99 TYR 0.009 0.002 TYR A 313 ARG 0.002 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05340 ( 466) hydrogen bonds : angle 4.20749 ( 1368) covalent geometry : bond 0.00421 ( 5830) covalent geometry : angle 0.54732 ( 7946) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7885 (pp20) cc_final: 0.7679 (pp20) REVERT: A 403 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: B 59 GLU cc_start: 0.7915 (pp20) cc_final: 0.7702 (pp20) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 3.0320 time to fit residues: 202.5177 Evaluate side-chains 59 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.068436 restraints weight = 23054.065| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.27 r_work: 0.2706 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5830 Z= 0.175 Angle : 0.506 4.359 7946 Z= 0.265 Chirality : 0.037 0.129 978 Planarity : 0.004 0.032 974 Dihedral : 4.360 29.805 782 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.62 % Allowed : 11.81 % Favored : 86.57 % 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: 3.64 (0.32), residues: 726 helix: 2.61 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.35 (0.69), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.002 TYR B 359 ARG 0.003 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 466) hydrogen bonds : angle 4.02246 ( 1368) covalent geometry : bond 0.00403 ( 5830) covalent geometry : angle 0.50563 ( 7946) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.855 Fit side-chains REVERT: A 59 GLU cc_start: 0.7908 (pp20) cc_final: 0.7673 (pp20) REVERT: A 289 LYS cc_start: 0.9028 (mppt) cc_final: 0.8785 (mtmm) REVERT: B 59 GLU cc_start: 0.7916 (pp20) cc_final: 0.7692 (pp20) REVERT: B 289 LYS cc_start: 0.9032 (mppt) cc_final: 0.8775 (mtmm) outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 3.0434 time to fit residues: 190.5920 Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 55 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069705 restraints weight = 23031.971| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.26 r_work: 0.2725 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5830 Z= 0.119 Angle : 0.471 4.207 7946 Z= 0.247 Chirality : 0.035 0.128 978 Planarity : 0.003 0.031 974 Dihedral : 4.209 27.338 782 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.49 % Allowed : 13.11 % Favored : 86.41 % 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: 3.90 (0.32), residues: 726 helix: 2.84 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.17 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR A 313 ARG 0.002 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 466) hydrogen bonds : angle 3.93759 ( 1368) covalent geometry : bond 0.00261 ( 5830) covalent geometry : angle 0.47108 ( 7946) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.908 Fit side-chains REVERT: A 59 GLU cc_start: 0.7883 (pp20) cc_final: 0.7650 (pp20) REVERT: A 289 LYS cc_start: 0.8984 (mppt) cc_final: 0.8695 (mtmm) REVERT: B 59 GLU cc_start: 0.7881 (pp20) cc_final: 0.7652 (pp20) REVERT: B 289 LYS cc_start: 0.8974 (mppt) cc_final: 0.8756 (mtmm) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 2.8174 time to fit residues: 168.2836 Evaluate side-chains 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068099 restraints weight = 23182.370| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.27 r_work: 0.2697 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.177 Angle : 0.496 4.694 7946 Z= 0.262 Chirality : 0.037 0.128 978 Planarity : 0.004 0.031 974 Dihedral : 3.963 23.746 780 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.78 % Allowed : 11.49 % Favored : 86.73 % 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: 3.92 (0.32), residues: 726 helix: 2.87 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.08 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.015 0.001 PHE B 99 TYR 0.010 0.002 TYR B 359 ARG 0.001 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.04949 ( 466) hydrogen bonds : angle 3.92841 ( 1368) covalent geometry : bond 0.00408 ( 5830) covalent geometry : angle 0.49558 ( 7946) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.846 Fit side-chains REVERT: A 59 GLU cc_start: 0.7822 (pp20) cc_final: 0.7599 (pp20) REVERT: B 59 GLU cc_start: 0.7821 (pp20) cc_final: 0.7597 (pp20) REVERT: B 289 LYS cc_start: 0.9002 (mppt) cc_final: 0.8760 (mtmm) outliers start: 11 outliers final: 0 residues processed: 59 average time/residue: 3.0000 time to fit residues: 184.7262 Evaluate side-chains 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068603 restraints weight = 23316.370| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.28 r_work: 0.2710 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5830 Z= 0.142 Angle : 0.491 6.112 7946 Z= 0.259 Chirality : 0.036 0.129 978 Planarity : 0.004 0.028 974 Dihedral : 3.933 23.631 780 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.65 % Allowed : 12.14 % Favored : 87.22 % 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: 3.99 (0.32), residues: 726 helix: 2.93 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.05 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR A 313 ARG 0.001 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 466) hydrogen bonds : angle 3.91848 ( 1368) covalent geometry : bond 0.00323 ( 5830) covalent geometry : angle 0.49057 ( 7946) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.824 Fit side-chains REVERT: A 59 GLU cc_start: 0.7813 (pp20) cc_final: 0.7588 (pp20) REVERT: A 259 GLU cc_start: 0.8173 (mp0) cc_final: 0.7860 (mp0) REVERT: A 403 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 59 GLU cc_start: 0.7806 (pp20) cc_final: 0.7581 (pp20) REVERT: B 259 GLU cc_start: 0.8161 (mp0) cc_final: 0.7852 (mp0) REVERT: B 403 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8391 (mp0) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 2.8301 time to fit residues: 159.8109 Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066926 restraints weight = 23586.964| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.35 r_work: 0.2718 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.146 Angle : 0.490 6.668 7946 Z= 0.259 Chirality : 0.036 0.128 978 Planarity : 0.004 0.029 974 Dihedral : 3.899 23.334 780 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.32), residues: 726 helix: 3.00 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.10 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 466) hydrogen bonds : angle 3.90235 ( 1368) covalent geometry : bond 0.00335 ( 5830) covalent geometry : angle 0.49005 ( 7946) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.019 Fit side-chains REVERT: A 59 GLU cc_start: 0.7776 (pp20) cc_final: 0.7553 (pp20) REVERT: A 259 GLU cc_start: 0.7986 (mp0) cc_final: 0.7675 (mp0) REVERT: A 403 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: B 59 GLU cc_start: 0.7745 (pp20) cc_final: 0.7522 (pp20) REVERT: B 259 GLU cc_start: 0.7990 (mp0) cc_final: 0.7679 (mp0) REVERT: B 403 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8297 (mp0) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 3.4629 time to fit residues: 201.1456 Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069268 restraints weight = 22627.751| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.32 r_work: 0.2711 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.126 Angle : 0.488 7.056 7946 Z= 0.255 Chirality : 0.036 0.130 978 Planarity : 0.004 0.029 974 Dihedral : 3.844 22.909 780 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.97 % Allowed : 11.97 % Favored : 87.06 % 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: 4.22 (0.32), residues: 726 helix: 3.07 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.19 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE A 99 TYR 0.010 0.001 TYR A 313 ARG 0.002 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 466) hydrogen bonds : angle 3.85016 ( 1368) covalent geometry : bond 0.00283 ( 5830) covalent geometry : angle 0.48820 ( 7946) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 2.409 Fit side-chains REVERT: A 59 GLU cc_start: 0.7756 (pp20) cc_final: 0.7533 (pp20) REVERT: A 259 GLU cc_start: 0.7947 (mp0) cc_final: 0.7579 (mp0) REVERT: A 370 ARG cc_start: 0.7184 (tmm-80) cc_final: 0.6973 (tmm160) REVERT: B 59 GLU cc_start: 0.7715 (pp20) cc_final: 0.7482 (pp20) REVERT: B 259 GLU cc_start: 0.7950 (mp0) cc_final: 0.7582 (mp0) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 3.3013 time to fit residues: 191.6242 Evaluate side-chains 55 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.100340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.068582 restraints weight = 22619.356| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.31 r_work: 0.2700 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5830 Z= 0.167 Angle : 0.499 7.081 7946 Z= 0.262 Chirality : 0.036 0.127 978 Planarity : 0.004 0.029 974 Dihedral : 3.840 22.993 780 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.13 % Allowed : 11.97 % Favored : 86.89 % 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: 4.20 (0.32), residues: 726 helix: 3.05 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.21 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.002 TYR B 359 ARG 0.001 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 466) hydrogen bonds : angle 3.87661 ( 1368) covalent geometry : bond 0.00387 ( 5830) covalent geometry : angle 0.49892 ( 7946) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 1.092 Fit side-chains REVERT: A 59 GLU cc_start: 0.7705 (pp20) cc_final: 0.7465 (pp20) REVERT: A 259 GLU cc_start: 0.7984 (mp0) cc_final: 0.7644 (mp0) REVERT: B 59 GLU cc_start: 0.7700 (pp20) cc_final: 0.7464 (pp20) REVERT: B 259 GLU cc_start: 0.7991 (mp0) cc_final: 0.7650 (mp0) outliers start: 7 outliers final: 2 residues processed: 56 average time/residue: 3.7581 time to fit residues: 220.6669 Evaluate side-chains 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.101247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.069827 restraints weight = 22563.325| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.30 r_work: 0.2720 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.119 Angle : 0.484 7.388 7946 Z= 0.252 Chirality : 0.035 0.125 978 Planarity : 0.004 0.029 974 Dihedral : 3.800 22.811 780 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.65 % Allowed : 12.62 % Favored : 86.73 % 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: 4.32 (0.32), residues: 726 helix: 3.15 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.14 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.010 0.001 TYR A 313 ARG 0.001 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 466) hydrogen bonds : angle 3.82220 ( 1368) covalent geometry : bond 0.00263 ( 5830) covalent geometry : angle 0.48401 ( 7946) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.429 Fit side-chains REVERT: A 59 GLU cc_start: 0.7710 (pp20) cc_final: 0.7476 (pp20) REVERT: A 259 GLU cc_start: 0.7983 (mp0) cc_final: 0.7667 (mp0) REVERT: B 59 GLU cc_start: 0.7704 (pp20) cc_final: 0.7470 (pp20) REVERT: B 259 GLU cc_start: 0.7981 (mp0) cc_final: 0.7676 (mp0) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 3.3941 time to fit residues: 191.4347 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.101558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070183 restraints weight = 22583.530| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.29 r_work: 0.2732 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.116 Angle : 0.473 6.262 7946 Z= 0.245 Chirality : 0.035 0.127 978 Planarity : 0.004 0.029 974 Dihedral : 3.747 22.419 780 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.32 % Allowed : 13.43 % Favored : 86.25 % 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: 4.43 (0.32), residues: 726 helix: 3.22 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.23 (0.66), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.001 PHE A 99 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 466) hydrogen bonds : angle 3.78775 ( 1368) covalent geometry : bond 0.00261 ( 5830) covalent geometry : angle 0.47277 ( 7946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10472.46 seconds wall clock time: 186 minutes 34.48 seconds (11194.48 seconds total)