Starting phenix.real_space_refine on Wed Mar 4 07:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_26626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_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 { model { file = "/net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_26626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_26626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_26626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unl_26626/03_2026/7unl_26626.map" } resolution = 2.45 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= 0.035 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.19, per 1000 atoms: 0.19 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: 0.89 Conformation dependent library (CDL) restraints added in 341.0 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: 0.24 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: 2.98 Time building geometry restraints manager: 1.27 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 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: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 339 TYR 0.011 0.002 TYR A 81 PHE 0.054 0.002 PHE A 314 TRP 0.014 0.002 TRP B 394 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5830) covalent geometry : angle 0.55894 ( 7946) hydrogen bonds : bond 0.12518 ( 466) hydrogen bonds : angle 5.59831 ( 1368) *********************** 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 : 0.303 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: 1.0732 time to fit residues: 111.4686 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 : 0.275 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.101684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.069194 restraints weight = 22634.676| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.31 r_work: 0.2760 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5830 Z= 0.173 Angle : 0.537 4.804 7946 Z= 0.285 Chirality : 0.037 0.129 978 Planarity : 0.004 0.032 974 Dihedral : 4.593 34.408 782 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.46 % Allowed : 13.27 % Favored : 85.28 % 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 are not related in a simple way. whole: 3.48 (0.33), residues: 726 helix: 2.42 (0.21), residues: 606 sheet: None (None), residues: 0 loop : 1.91 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 377 TYR 0.010 0.002 TYR A 359 PHE 0.014 0.001 PHE A 99 TRP 0.011 0.002 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5830) covalent geometry : angle 0.53720 ( 7946) hydrogen bonds : bond 0.05382 ( 466) hydrogen bonds : angle 4.21552 ( 1368) *********************** 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 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.304 Fit side-chains REVERT: A 403 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 59 GLU cc_start: 0.7875 (pp20) cc_final: 0.7666 (pp20) REVERT: B 67 ASP cc_start: 0.7894 (m-30) cc_final: 0.7488 (m-30) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 1.2340 time to fit residues: 95.2652 Evaluate side-chains 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.100999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.069694 restraints weight = 23005.668| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.28 r_work: 0.2732 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2126 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= 0.140 Angle : 0.492 4.364 7946 Z= 0.257 Chirality : 0.036 0.126 978 Planarity : 0.004 0.032 974 Dihedral : 4.368 31.039 782 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.13 % Allowed : 13.11 % Favored : 85.76 % 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 are not related in a simple way. whole: 3.72 (0.33), residues: 726 helix: 2.65 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.52 (0.70), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.009 0.001 TYR A 359 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5830) covalent geometry : angle 0.49197 ( 7946) hydrogen bonds : bond 0.04903 ( 466) hydrogen bonds : angle 4.03779 ( 1368) *********************** 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 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.204 Fit side-chains REVERT: A 67 ASP cc_start: 0.7845 (m-30) cc_final: 0.7442 (m-30) REVERT: A 289 LYS cc_start: 0.8989 (mppt) cc_final: 0.8779 (mtmm) REVERT: B 59 GLU cc_start: 0.7906 (pp20) cc_final: 0.7700 (pp20) REVERT: B 67 ASP cc_start: 0.7869 (m-30) cc_final: 0.7425 (m-30) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 1.1237 time to fit residues: 89.5424 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.0870 chunk 26 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.101368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.070247 restraints weight = 22914.245| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.26 r_work: 0.2739 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5830 Z= 0.128 Angle : 0.487 4.256 7946 Z= 0.253 Chirality : 0.035 0.130 978 Planarity : 0.003 0.031 974 Dihedral : 4.220 27.806 782 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.62 % Allowed : 13.43 % Favored : 84.95 % 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 are not related in a simple way. whole: 3.97 (0.32), residues: 726 helix: 2.88 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.21 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.010 0.001 TYR A 313 PHE 0.013 0.001 PHE A 99 TRP 0.009 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5830) covalent geometry : angle 0.48688 ( 7946) hydrogen bonds : bond 0.04558 ( 466) hydrogen bonds : angle 3.90130 ( 1368) *********************** 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 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.329 Fit side-chains REVERT: A 67 ASP cc_start: 0.7807 (m-30) cc_final: 0.7386 (m-30) REVERT: B 59 GLU cc_start: 0.7899 (pp20) cc_final: 0.7679 (pp20) REVERT: B 67 ASP cc_start: 0.7851 (m-30) cc_final: 0.7429 (m-30) outliers start: 10 outliers final: 2 residues processed: 73 average time/residue: 1.0575 time to fit residues: 81.1706 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.098979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.066380 restraints weight = 23080.376| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.33 r_work: 0.2713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2596 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= 0.188 Angle : 0.516 4.851 7946 Z= 0.274 Chirality : 0.037 0.128 978 Planarity : 0.004 0.030 974 Dihedral : 3.983 23.685 780 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.81 % Allowed : 12.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.99 (0.32), residues: 726 helix: 2.89 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.27 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 370 TYR 0.010 0.002 TYR A 313 PHE 0.015 0.001 PHE B 99 TRP 0.010 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 5830) covalent geometry : angle 0.51616 ( 7946) hydrogen bonds : bond 0.04990 ( 466) hydrogen bonds : angle 3.92292 ( 1368) *********************** 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 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.275 Fit side-chains REVERT: A 67 ASP cc_start: 0.7782 (m-30) cc_final: 0.7368 (m-30) REVERT: B 59 GLU cc_start: 0.7772 (pp20) cc_final: 0.7556 (pp20) REVERT: B 67 ASP cc_start: 0.7805 (m-30) cc_final: 0.7388 (m-30) outliers start: 5 outliers final: 1 residues processed: 68 average time/residue: 1.1166 time to fit residues: 79.6715 Evaluate side-chains 65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068984 restraints weight = 23292.594| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.27 r_work: 0.2717 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.145 Angle : 0.506 6.013 7946 Z= 0.266 Chirality : 0.036 0.128 978 Planarity : 0.003 0.031 974 Dihedral : 3.955 23.611 780 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.97 % Allowed : 12.94 % Favored : 86.08 % 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 are not related in a simple way. whole: 4.10 (0.32), residues: 726 helix: 2.99 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.18 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 370 TYR 0.009 0.001 TYR A 313 PHE 0.012 0.001 PHE B 99 TRP 0.010 0.002 TRP B 394 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5830) covalent geometry : angle 0.50635 ( 7946) hydrogen bonds : bond 0.04669 ( 466) hydrogen bonds : angle 3.90389 ( 1368) *********************** 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 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.313 Fit side-chains REVERT: A 67 ASP cc_start: 0.7790 (m-30) cc_final: 0.7369 (m-30) REVERT: A 259 GLU cc_start: 0.8210 (mp0) cc_final: 0.7902 (mp0) REVERT: B 59 GLU cc_start: 0.7827 (pp20) cc_final: 0.7606 (pp20) REVERT: B 67 ASP cc_start: 0.7818 (m-30) cc_final: 0.7393 (m-30) REVERT: B 259 GLU cc_start: 0.8195 (mp0) cc_final: 0.7885 (mp0) outliers start: 6 outliers final: 1 residues processed: 70 average time/residue: 1.2597 time to fit residues: 92.1084 Evaluate side-chains 61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.101599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.069861 restraints weight = 22403.616| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.31 r_work: 0.2719 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2837 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= 0.118 Angle : 0.488 6.818 7946 Z= 0.257 Chirality : 0.035 0.127 978 Planarity : 0.004 0.030 974 Dihedral : 3.889 22.952 780 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.49 % Allowed : 13.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.25 (0.32), residues: 726 helix: 3.10 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.12 (0.66), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.010 0.001 TYR A 313 PHE 0.012 0.001 PHE B 99 TRP 0.009 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5830) covalent geometry : angle 0.48832 ( 7946) hydrogen bonds : bond 0.04340 ( 466) hydrogen bonds : angle 3.84131 ( 1368) *********************** 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 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.262 Fit side-chains REVERT: A 67 ASP cc_start: 0.7738 (m-30) cc_final: 0.7328 (m-30) REVERT: A 259 GLU cc_start: 0.7931 (mp0) cc_final: 0.7632 (mp0) REVERT: B 59 GLU cc_start: 0.7769 (pp20) cc_final: 0.7554 (pp20) REVERT: B 67 ASP cc_start: 0.7725 (m-30) cc_final: 0.7341 (m-30) REVERT: B 259 GLU cc_start: 0.7936 (mp0) cc_final: 0.7637 (mp0) outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 1.1981 time to fit residues: 82.7729 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR 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 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.101001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.069770 restraints weight = 22513.208| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.28 r_work: 0.2718 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5830 Z= 0.127 Angle : 0.494 6.817 7946 Z= 0.259 Chirality : 0.035 0.127 978 Planarity : 0.004 0.030 974 Dihedral : 3.844 22.663 780 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.97 % Allowed : 13.11 % Favored : 85.92 % 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 are not related in a simple way. whole: 4.29 (0.32), residues: 726 helix: 3.11 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.20 (0.66), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 370 TYR 0.009 0.001 TYR A 313 PHE 0.013 0.001 PHE B 99 TRP 0.009 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5830) covalent geometry : angle 0.49376 ( 7946) hydrogen bonds : bond 0.04340 ( 466) hydrogen bonds : angle 3.81999 ( 1368) *********************** 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 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.305 Fit side-chains REVERT: A 67 ASP cc_start: 0.7723 (m-30) cc_final: 0.7337 (m-30) REVERT: A 259 GLU cc_start: 0.7957 (mp0) cc_final: 0.7677 (mp0) REVERT: A 403 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: B 59 GLU cc_start: 0.7742 (pp20) cc_final: 0.7523 (pp20) REVERT: B 67 ASP cc_start: 0.7700 (m-30) cc_final: 0.7319 (m-30) REVERT: B 259 GLU cc_start: 0.7962 (mp0) cc_final: 0.7680 (mp0) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.1920 time to fit residues: 86.1186 Evaluate side-chains 65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 426 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.101161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.069641 restraints weight = 22528.659| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.29 r_work: 0.2719 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5830 Z= 0.132 Angle : 0.498 7.141 7946 Z= 0.261 Chirality : 0.035 0.127 978 Planarity : 0.004 0.030 974 Dihedral : 3.812 22.620 780 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.65 % Allowed : 13.75 % Favored : 85.60 % 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 are not related in a simple way. whole: 4.32 (0.32), residues: 726 helix: 3.13 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.22 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.009 0.001 TYR A 313 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5830) covalent geometry : angle 0.49837 ( 7946) hydrogen bonds : bond 0.04334 ( 466) hydrogen bonds : angle 3.81016 ( 1368) *********************** 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 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.302 Fit side-chains REVERT: A 67 ASP cc_start: 0.7683 (m-30) cc_final: 0.7299 (m-30) REVERT: A 259 GLU cc_start: 0.7962 (mp0) cc_final: 0.7636 (mp0) REVERT: B 59 GLU cc_start: 0.7732 (pp20) cc_final: 0.7499 (pp20) REVERT: B 67 ASP cc_start: 0.7706 (m-30) cc_final: 0.7322 (m-30) REVERT: B 259 GLU cc_start: 0.7973 (mp0) cc_final: 0.7644 (mp0) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.2638 time to fit residues: 84.5004 Evaluate side-chains 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.102339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.070862 restraints weight = 22752.736| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.31 r_work: 0.2737 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5830 Z= 0.109 Angle : 0.492 7.126 7946 Z= 0.255 Chirality : 0.035 0.127 978 Planarity : 0.004 0.030 974 Dihedral : 3.761 22.260 780 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.81 % Allowed : 13.27 % Favored : 85.92 % 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 are not related in a simple way. whole: 4.45 (0.32), residues: 726 helix: 3.22 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.25 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 370 TYR 0.010 0.001 TYR A 313 PHE 0.011 0.001 PHE B 99 TRP 0.009 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5830) covalent geometry : angle 0.49172 ( 7946) hydrogen bonds : bond 0.04040 ( 466) hydrogen bonds : angle 3.77834 ( 1368) ********************** 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 70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.231 Fit side-chains REVERT: A 67 ASP cc_start: 0.7673 (m-30) cc_final: 0.7289 (m-30) REVERT: A 259 GLU cc_start: 0.7964 (mp0) cc_final: 0.7658 (mp0) REVERT: B 59 GLU cc_start: 0.7739 (pp20) cc_final: 0.7508 (pp20) REVERT: B 67 ASP cc_start: 0.7682 (m-30) cc_final: 0.7320 (m-30) REVERT: B 259 GLU cc_start: 0.7975 (mp0) cc_final: 0.7666 (mp0) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 1.1881 time to fit residues: 80.8758 Evaluate side-chains 60 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.069595 restraints weight = 22468.141| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.30 r_work: 0.2713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5830 Z= 0.150 Angle : 0.513 7.202 7946 Z= 0.266 Chirality : 0.036 0.127 978 Planarity : 0.004 0.029 974 Dihedral : 3.759 22.327 780 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 14.56 % Favored : 84.95 % 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 are not related in a simple way. whole: 4.39 (0.32), residues: 726 helix: 3.18 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.24 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 370 TYR 0.009 0.001 TYR B 359 PHE 0.014 0.001 PHE B 99 TRP 0.009 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5830) covalent geometry : angle 0.51305 ( 7946) hydrogen bonds : bond 0.04371 ( 466) hydrogen bonds : angle 3.79473 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4356.10 seconds wall clock time: 74 minutes 20.79 seconds (4460.79 seconds total)