Starting phenix.real_space_refine on Wed Jun 3 11:11:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.map" model { file = "/net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc2_70307/06_2026/9oc2_70307.cif" } resolution = 2.69 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= 0.014 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 Ca 1 9.91 5 P 4 5.49 5 S 26 5.16 5 C 2662 2.51 5 N 574 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 909 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 921 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 909 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 921 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.04, per 1000 atoms: 0.26 Number of scatterers: 3950 At special positions: 0 Unit cell: (66.36, 71.4, 65.52, 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) Ca 1 19.99 S 26 16.00 P 4 15.00 O 683 8.00 N 574 7.00 C 2662 6.00 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: 0.38 Conformation dependent library (CDL) restraints added in 128.7 milliseconds 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.958A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.551A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.617A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.633A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.908A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.957A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.551A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.617A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 removed outlier: 3.633A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.908A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 918 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: 0.59 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 570 1.33 - 1.45: 1076 1.45 - 1.57: 2304 1.57 - 1.69: 8 1.69 - 1.81: 50 Bond restraints: 4008 Sorted by residual: bond pdb=" N GLN C 556 " pdb=" CA GLN C 556 " ideal model delta sigma weight residual 1.462 1.485 -0.023 8.50e-03 1.38e+04 7.59e+00 bond pdb=" N GLN A 556 " pdb=" CA GLN A 556 " ideal model delta sigma weight residual 1.462 1.485 -0.023 8.50e-03 1.38e+04 7.34e+00 bond pdb=" N VAL A 820 " pdb=" CA VAL A 820 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.25e+00 bond pdb=" N ILE D 837 " pdb=" CA ILE D 837 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.18e-02 7.18e+03 6.79e+00 bond pdb=" N VAL C 820 " pdb=" CA VAL C 820 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.19e-02 7.06e+03 6.66e+00 ... (remaining 4003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 5237 0.88 - 1.76: 126 1.76 - 2.64: 55 2.64 - 3.52: 24 3.52 - 4.40: 6 Bond angle restraints: 5448 Sorted by residual: angle pdb=" CA PHE C 558 " pdb=" CB PHE C 558 " pdb=" CG PHE C 558 " ideal model delta sigma weight residual 113.80 117.22 -3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" N MET C 818 " pdb=" CA MET C 818 " pdb=" C MET C 818 " ideal model delta sigma weight residual 112.54 108.58 3.96 1.22e+00 6.72e-01 1.05e+01 angle pdb=" N MET A 818 " pdb=" CA MET A 818 " pdb=" C MET A 818 " ideal model delta sigma weight residual 112.54 108.71 3.83 1.22e+00 6.72e-01 9.84e+00 angle pdb=" CA ILE D 837 " pdb=" C ILE D 837 " pdb=" O ILE D 837 " ideal model delta sigma weight residual 121.29 118.02 3.27 1.07e+00 8.73e-01 9.35e+00 angle pdb=" N MET C 555 " pdb=" CA MET C 555 " pdb=" C MET C 555 " ideal model delta sigma weight residual 113.02 109.37 3.65 1.20e+00 6.94e-01 9.26e+00 ... (remaining 5443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 2286 16.51 - 33.02: 95 33.02 - 49.53: 10 49.53 - 66.05: 14 66.05 - 82.56: 7 Dihedral angle restraints: 2412 sinusoidal: 950 harmonic: 1462 Sorted by residual: dihedral pdb=" CA LEU C 819 " pdb=" CB LEU C 819 " pdb=" CG LEU C 819 " pdb=" CD1 LEU C 819 " ideal model delta sinusoidal sigma weight residual 180.00 147.01 32.99 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" C12 POV A 902 " pdb=" C11 POV A 902 " pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sinusoidal sigma weight residual 46.81 129.37 -82.56 2 3.00e+01 1.11e-03 5.24e+00 dihedral pdb=" C12 POV C 902 " pdb=" C11 POV C 902 " pdb=" O12 POV C 902 " pdb=" P POV C 902 " ideal model delta sinusoidal sigma weight residual 46.81 128.90 -82.09 2 3.00e+01 1.11e-03 5.23e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 500 0.036 - 0.071: 127 0.071 - 0.107: 16 0.107 - 0.142: 9 0.142 - 0.178: 8 Chirality restraints: 660 Sorted by residual: chirality pdb=" CA ILE D 837 " pdb=" N ILE D 837 " pdb=" C ILE D 837 " pdb=" CB ILE D 837 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA ILE B 837 " pdb=" N ILE B 837 " pdb=" C ILE B 837 " pdb=" CB ILE B 837 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA MET A 818 " pdb=" N MET A 818 " pdb=" C MET A 818 " pdb=" CB MET A 818 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 657 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 817 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C PHE C 817 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE C 817 " 0.015 2.00e-02 2.50e+03 pdb=" N MET C 818 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 817 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C PHE A 817 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE A 817 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 818 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.33e-01 pdb=" N PRO B 553 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.013 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 707 2.77 - 3.30: 3882 3.30 - 3.84: 6099 3.84 - 4.37: 7488 4.37 - 4.90: 12755 Nonbonded interactions: 30931 Sorted by model distance: nonbonded pdb=" ND2 ASN B 616 " pdb=" O HOH B1001 " model vdw 2.240 3.120 nonbonded pdb=" O PHE B 614 " pdb=" O HOH B1002 " model vdw 2.311 3.040 nonbonded pdb=" ND2 ASN D 616 " pdb=" O HOH D1001 " model vdw 2.312 3.120 nonbonded pdb=" O HOH D1001 " pdb=" O HOH D1007 " model vdw 2.362 3.040 nonbonded pdb=" O ASN D 616 " pdb=" O HOH D1002 " model vdw 2.373 3.040 ... (remaining 30926 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 546 through 901) selection = chain 'D' } 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: 6.200 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 0.032 4008 Z= 0.189 Angle : 0.435 4.396 5448 Z= 0.286 Chirality : 0.038 0.178 660 Planarity : 0.003 0.023 624 Dihedral : 11.410 82.557 1456 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.02 (0.34), residues: 486 helix: 1.12 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -1.06 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.002 0.001 TYR B 646 PHE 0.007 0.001 PHE D 642 TRP 0.003 0.001 TRP B 607 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.19 ( 4008) covalent geometry : angle 0.43550 / 0.29 ( 5448) hydrogen bonds : bond 0.24453 / 16.57 ( 306) hydrogen bonds : angle 5.50524 / 4.08 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3116 time to fit residues: 29.0952 Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 812 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131889 restraints weight = 4345.362| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.69 r_work: 0.3379 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4008 Z= 0.148 Angle : 0.480 4.613 5448 Z= 0.260 Chirality : 0.036 0.128 660 Planarity : 0.004 0.024 624 Dihedral : 13.008 85.906 812 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.43 % Allowed : 9.71 % Favored : 86.86 % 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: 2.44 (0.35), residues: 486 helix: 2.03 (0.23), residues: 404 sheet: None (None), residues: 0 loop : -0.37 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.005 0.001 TYR C 647 PHE 0.024 0.002 PHE B 836 TRP 0.007 0.001 TRP C 563 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 4008) covalent geometry : angle 0.48034 / 0.26 ( 5448) hydrogen bonds : bond 0.06490 / 4.44 ( 306) hydrogen bonds : angle 3.33125 / 2.45 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.134 Fit side-chains REVERT: C 607 MET cc_start: 0.8422 (mmt) cc_final: 0.8212 (mmm) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.3972 time to fit residues: 30.2255 Evaluate side-chains 72 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 14 optimal weight: 0.7980 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.163308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131887 restraints weight = 4365.330| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.71 r_work: 0.3345 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4008 Z= 0.140 Angle : 0.462 4.647 5448 Z= 0.248 Chirality : 0.035 0.123 660 Planarity : 0.003 0.024 624 Dihedral : 12.946 89.335 812 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.29 % Allowed : 11.43 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.35), residues: 486 helix: 2.55 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -1.07 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 582 TYR 0.005 0.001 TYR C 647 PHE 0.027 0.002 PHE B 836 TRP 0.008 0.001 TRP B 635 HIS 0.000 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4008) covalent geometry : angle 0.46183 / 0.25 ( 5448) hydrogen bonds : bond 0.05860 / 4.01 ( 306) hydrogen bonds : angle 3.11896 / 2.28 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.146 Fit side-chains REVERT: C 607 MET cc_start: 0.8404 (mmt) cc_final: 0.8187 (mmm) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.3985 time to fit residues: 30.8297 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.0010 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.164437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133088 restraints weight = 4182.152| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.70 r_work: 0.3382 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.002 0.022 4008 Z= 0.116 Angle : 0.423 4.701 5448 Z= 0.228 Chirality : 0.034 0.119 660 Planarity : 0.003 0.022 624 Dihedral : 12.660 89.164 812 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.43 % Allowed : 11.43 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.35), residues: 486 helix: 2.87 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.94 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.003 0.001 TYR A 578 PHE 0.026 0.002 PHE B 836 TRP 0.007 0.001 TRP C 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 4008) covalent geometry : angle 0.42308 / 0.23 ( 5448) hydrogen bonds : bond 0.05046 / 3.45 ( 306) hydrogen bonds : angle 2.95221 / 2.15 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.136 Fit side-chains REVERT: A 607 MET cc_start: 0.8339 (mmm) cc_final: 0.8097 (mmt) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 0.3619 time to fit residues: 31.0473 Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 626 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.163566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131994 restraints weight = 4240.065| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.72 r_work: 0.3391 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4008 Z= 0.124 Angle : 0.436 4.661 5448 Z= 0.235 Chirality : 0.034 0.120 660 Planarity : 0.003 0.022 624 Dihedral : 12.542 89.425 812 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.57 % Allowed : 15.43 % Favored : 80.00 % 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: 3.46 (0.36), residues: 486 helix: 2.95 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.87 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.004 0.001 TYR C 578 PHE 0.029 0.002 PHE B 836 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4008) covalent geometry : angle 0.43613 / 0.24 ( 5448) hydrogen bonds : bond 0.05266 / 3.60 ( 306) hydrogen bonds : angle 2.92806 / 2.13 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.129 Fit side-chains REVERT: A 607 MET cc_start: 0.8362 (mmm) cc_final: 0.8148 (mmt) outliers start: 16 outliers final: 8 residues processed: 79 average time/residue: 0.3446 time to fit residues: 28.5510 Evaluate side-chains 76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132918 restraints weight = 4256.958| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.71 r_work: 0.3387 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4008 Z= 0.124 Angle : 0.434 4.651 5448 Z= 0.234 Chirality : 0.035 0.120 660 Planarity : 0.003 0.021 624 Dihedral : 12.449 87.532 812 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.14 % Allowed : 16.86 % Favored : 80.00 % 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: 3.50 (0.36), residues: 486 helix: 2.97 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.84 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.004 0.001 TYR C 578 PHE 0.026 0.002 PHE B 836 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4008) covalent geometry : angle 0.43425 / 0.23 ( 5448) hydrogen bonds : bond 0.05230 / 3.58 ( 306) hydrogen bonds : angle 2.92226 / 2.12 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.148 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.3699 time to fit residues: 29.8427 Evaluate side-chains 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 817 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127922 restraints weight = 4339.195| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.75 r_work: 0.3279 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4008 Z= 0.127 Angle : 0.440 4.663 5448 Z= 0.236 Chirality : 0.035 0.123 660 Planarity : 0.003 0.021 624 Dihedral : 12.408 86.673 812 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.43 % Allowed : 16.86 % Favored : 79.71 % 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: 3.52 (0.36), residues: 486 helix: 2.97 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -0.87 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.004 0.001 TYR C 647 PHE 0.025 0.002 PHE B 836 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 4008) covalent geometry : angle 0.44005 / 0.24 ( 5448) hydrogen bonds : bond 0.05325 / 3.64 ( 306) hydrogen bonds : angle 2.94494 / 2.14 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.101 Fit side-chains REVERT: A 607 MET cc_start: 0.8381 (mmm) cc_final: 0.8177 (mmt) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.3890 time to fit residues: 30.9735 Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 817 ASN Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 817 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127413 restraints weight = 4290.147| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.76 r_work: 0.3284 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4008 Z= 0.129 Angle : 0.444 4.620 5448 Z= 0.238 Chirality : 0.035 0.122 660 Planarity : 0.003 0.021 624 Dihedral : 12.352 85.750 812 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.71 % Allowed : 16.86 % Favored : 79.43 % 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: 3.51 (0.35), residues: 486 helix: 2.97 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -0.87 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 582 TYR 0.004 0.001 TYR C 647 PHE 0.024 0.002 PHE B 836 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 4008) covalent geometry : angle 0.44413 / 0.24 ( 5448) hydrogen bonds : bond 0.05369 / 3.67 ( 306) hydrogen bonds : angle 2.94904 / 2.14 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.133 Fit side-chains REVERT: A 607 MET cc_start: 0.8349 (mmm) cc_final: 0.8143 (mmt) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.3618 time to fit residues: 29.0999 Evaluate side-chains 82 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 817 ASN Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 817 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 15 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 overall best weight: 0.2232 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.166112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134225 restraints weight = 4349.576| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.74 r_work: 0.3353 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4008 Z= 0.097 Angle : 0.394 4.644 5448 Z= 0.213 Chirality : 0.033 0.115 660 Planarity : 0.003 0.021 624 Dihedral : 11.899 85.122 812 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.43 % Allowed : 18.86 % Favored : 79.71 % 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: 4.05 (0.36), residues: 486 helix: 3.38 (0.23), residues: 398 sheet: None (None), residues: 0 loop : -1.01 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 582 TYR 0.002 0.001 TYR A 647 PHE 0.028 0.001 PHE B 836 TRP 0.006 0.001 TRP B 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.10 ( 4008) covalent geometry : angle 0.39420 / 0.21 ( 5448) hydrogen bonds : bond 0.04012 / 2.73 ( 306) hydrogen bonds : angle 2.72627 / 1.98 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.143 Fit side-chains REVERT: A 607 MET cc_start: 0.8388 (mmm) cc_final: 0.8155 (mmt) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.3560 time to fit residues: 27.1567 Evaluate side-chains 69 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.166141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133636 restraints weight = 4266.172| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.74 r_work: 0.3353 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4008 Z= 0.107 Angle : 0.412 4.586 5448 Z= 0.222 Chirality : 0.034 0.117 660 Planarity : 0.003 0.022 624 Dihedral : 11.870 84.140 812 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.14 % Allowed : 19.43 % Favored : 79.43 % 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: 3.89 (0.36), residues: 486 helix: 3.27 (0.23), residues: 398 sheet: None (None), residues: 0 loop : -1.09 (0.66), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.003 0.001 TYR A 647 PHE 0.030 0.001 PHE B 836 TRP 0.007 0.001 TRP C 563 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 4008) covalent geometry : angle 0.41171 / 0.22 ( 5448) hydrogen bonds : bond 0.04520 / 3.10 ( 306) hydrogen bonds : angle 2.78971 / 2.02 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 972 Ramachandran restraints generated. 486 Oldfield, 0 Emsley, 486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.139 Fit side-chains REVERT: A 564 LEU cc_start: 0.8509 (mp) cc_final: 0.8295 (tp) REVERT: A 607 MET cc_start: 0.8253 (mmm) cc_final: 0.8022 (mmt) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.3851 time to fit residues: 26.9357 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 816 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 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: D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129834 restraints weight = 4273.761| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.75 r_work: 0.3284 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4008 Z= 0.136 Angle : 0.456 4.669 5448 Z= 0.245 Chirality : 0.035 0.122 660 Planarity : 0.003 0.022 624 Dihedral : 12.178 85.371 812 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.43 % Allowed : 19.43 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.36), residues: 486 helix: 3.06 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -0.86 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.004 0.001 TYR C 647 PHE 0.031 0.002 PHE B 836 TRP 0.010 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 4008) covalent geometry : angle 0.45633 / 0.24 ( 5448) hydrogen bonds : bond 0.05531 / 3.79 ( 306) hydrogen bonds : angle 2.95210 / 2.14 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.96 seconds wall clock time: 27 minutes 50.11 seconds (1670.11 seconds total)