Starting phenix.real_space_refine on Wed Jul 1 23:43:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obz_70304/07_2026/9obz_70304.map" } resolution = 2.81 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= 0.010 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 32 5.16 5 C 2812 2.51 5 N 592 2.21 5 O 731 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4172 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 930 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1005 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 930 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1005 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.22, per 1000 atoms: 0.29 Number of scatterers: 4172 At special positions: 0 Unit cell: (69.72, 69.72, 68.04, 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 32 16.00 P 4 15.00 O 731 8.00 N 592 7.00 C 2812 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: 0.37 Conformation dependent library (CDL) restraints added in 91.6 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 76.3% 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: 3.682A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.087A 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 removed outlier: 3.564A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.684A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 580 removed outlier: 3.512A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.549A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 656 Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.592A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.767A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.276A 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: 3.629A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 580 removed outlier: 3.513A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.549A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 656 Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.537A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 906 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: 0.56 Time building geometry restraints manager: 0.45 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: 608 1.33 - 1.45: 1142 1.45 - 1.57: 2410 1.57 - 1.69: 8 1.69 - 1.81: 62 Bond restraints: 4230 Sorted by residual: bond pdb=" N GLN C 556 " pdb=" CA GLN C 556 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.11e+01 bond pdb=" N GLN A 556 " pdb=" CA GLN A 556 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" N GLN C 559 " pdb=" CA GLN C 559 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.14e+00 bond pdb=" N PHE A 558 " pdb=" CA PHE A 558 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.92e+00 bond pdb=" N PHE C 558 " pdb=" CA PHE C 558 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.19e-02 7.06e+03 6.76e+00 ... (remaining 4225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 5570 0.97 - 1.93: 101 1.93 - 2.90: 47 2.90 - 3.87: 7 3.87 - 4.83: 5 Bond angle restraints: 5730 Sorted by residual: angle pdb=" N MET C 555 " pdb=" CA MET C 555 " pdb=" C MET C 555 " ideal model delta sigma weight residual 113.16 108.47 4.69 1.24e+00 6.50e-01 1.43e+01 angle pdb=" N MET A 555 " pdb=" CA MET A 555 " pdb=" C MET A 555 " ideal model delta sigma weight residual 113.16 108.84 4.32 1.24e+00 6.50e-01 1.21e+01 angle pdb=" CA PHE A 558 " pdb=" CB PHE A 558 " pdb=" CG PHE A 558 " ideal model delta sigma weight residual 113.80 117.21 -3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" CA GLN C 559 " pdb=" C GLN C 559 " pdb=" O GLN C 559 " ideal model delta sigma weight residual 121.81 118.13 3.68 1.18e+00 7.18e-01 9.74e+00 angle pdb=" CA PHE A 558 " pdb=" C PHE A 558 " pdb=" O PHE A 558 " ideal model delta sigma weight residual 121.11 117.82 3.29 1.13e+00 7.83e-01 8.47e+00 ... (remaining 5725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2387 16.44 - 32.88: 104 32.88 - 49.32: 41 49.32 - 65.76: 10 65.76 - 82.20: 4 Dihedral angle restraints: 2546 sinusoidal: 1054 harmonic: 1492 Sorted by residual: dihedral pdb=" CA LEU D 566 " pdb=" CB LEU D 566 " pdb=" CG LEU D 566 " pdb=" CD1 LEU D 566 " ideal model delta sinusoidal sigma weight residual 180.00 142.25 37.75 3 1.50e+01 4.44e-03 6.61e+00 dihedral pdb=" CA LEU B 566 " pdb=" CB LEU B 566 " pdb=" CG LEU B 566 " pdb=" CD1 LEU B 566 " ideal model delta sinusoidal sigma weight residual 180.00 144.51 35.49 3 1.50e+01 4.44e-03 6.09e+00 dihedral pdb=" N MET A 813 " pdb=" CA MET A 813 " pdb=" CB MET A 813 " pdb=" CG MET A 813 " ideal model delta sinusoidal sigma weight residual 180.00 -147.54 -32.46 3 1.50e+01 4.44e-03 5.35e+00 ... (remaining 2543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 568 0.047 - 0.095: 94 0.095 - 0.142: 10 0.142 - 0.189: 5 0.189 - 0.237: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA LEU A 819 " pdb=" N LEU A 819 " pdb=" C LEU A 819 " pdb=" CB LEU A 819 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET C 555 " pdb=" N MET C 555 " pdb=" C MET C 555 " pdb=" CB MET C 555 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA LEU C 819 " pdb=" N LEU C 819 " pdb=" C LEU C 819 " pdb=" CB LEU C 819 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 675 not shown) Planarity restraints: 654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO D 553 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 553 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 553 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C SER A 553 " 0.018 2.00e-02 2.50e+03 pdb=" O SER A 553 " -0.007 2.00e-02 2.50e+03 pdb=" N PHE A 554 " -0.006 2.00e-02 2.50e+03 ... (remaining 651 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 500 2.75 - 3.29: 4130 3.29 - 3.83: 6485 3.83 - 4.36: 8001 4.36 - 4.90: 13669 Nonbonded interactions: 32785 Sorted by model distance: nonbonded pdb=" O HOH D1008 " pdb=" O HOH D1011 " model vdw 2.214 3.040 nonbonded pdb=" O HOH B1008 " pdb=" O HOH B1013 " model vdw 2.232 3.040 nonbonded pdb=" O LEU C 580 " pdb=" OG SER C 584 " model vdw 2.276 3.040 nonbonded pdb=" ND2 ASN C 616 " pdb=" OG SER D 617 " model vdw 2.323 3.120 nonbonded pdb=" ND2 ASN A 616 " pdb=" OG SER B 617 " model vdw 2.329 3.120 ... (remaining 32780 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 549 through 901) 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: 5.970 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.002 0.035 4230 Z= 0.172 Angle : 0.423 4.832 5730 Z= 0.276 Chirality : 0.036 0.237 678 Planarity : 0.003 0.030 654 Dihedral : 11.961 82.199 1570 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.25 % Allowed : 1.52 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.34), residues: 496 helix: 0.48 (0.24), residues: 376 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 120 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 0.006 0.001 PHE A 554 TRP 0.004 0.001 TRP B 635 HIS 0.001 0.000 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.17 ( 4230) covalent geometry : angle 0.42262 / 0.28 ( 5730) hydrogen bonds : bond 0.26167 / 17.11 ( 304) hydrogen bonds : angle 6.06641 / 4.43 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.144 Fit side-chains REVERT: B 565 MET cc_start: 0.8093 (mmt) cc_final: 0.7833 (mmt) REVERT: B 631 MET cc_start: 0.8345 (tpt) cc_final: 0.8076 (tpt) REVERT: B 817 ASN cc_start: 0.8258 (m-40) cc_final: 0.7944 (m-40) REVERT: D 565 MET cc_start: 0.7886 (mmt) cc_final: 0.7639 (mmt) REVERT: D 817 ASN cc_start: 0.8268 (m-40) cc_final: 0.7930 (m-40) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.3367 time to fit residues: 32.1935 Evaluate side-chains 78 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 656 GLN C 616 ASN D 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120689 restraints weight = 4600.290| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.53 r_work: 0.3175 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4230 Z= 0.166 Angle : 0.509 5.300 5730 Z= 0.275 Chirality : 0.036 0.127 678 Planarity : 0.004 0.033 654 Dihedral : 14.295 88.745 822 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 8.63 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.37), residues: 496 helix: 1.85 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.96 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 630 TYR 0.006 0.001 TYR B 646 PHE 0.015 0.002 PHE A 627 TRP 0.012 0.002 TRP D 635 HIS 0.004 0.002 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 4230) covalent geometry : angle 0.50859 / 0.27 ( 5730) hydrogen bonds : bond 0.07002 / 4.56 ( 304) hydrogen bonds : angle 3.63287 / 2.63 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.125 Fit side-chains REVERT: B 565 MET cc_start: 0.8306 (mmt) cc_final: 0.8089 (mmt) REVERT: C 819 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7038 (mp) REVERT: D 565 MET cc_start: 0.8139 (mmt) cc_final: 0.7938 (mmt) REVERT: D 833 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6894 (tm) outliers start: 7 outliers final: 0 residues processed: 81 average time/residue: 0.4078 time to fit residues: 34.4156 Evaluate side-chains 76 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN B 621 GLN C 559 GLN C 616 ASN D 817 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120561 restraints weight = 4547.748| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.46 r_work: 0.3193 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4230 Z= 0.148 Angle : 0.465 5.050 5730 Z= 0.251 Chirality : 0.035 0.128 678 Planarity : 0.004 0.033 654 Dihedral : 14.444 87.295 822 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.28 % Allowed : 9.64 % Favored : 88.07 % 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: 2.11 (0.38), residues: 496 helix: 2.09 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.81 (0.59), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 582 TYR 0.005 0.001 TYR B 646 PHE 0.013 0.001 PHE A 627 TRP 0.011 0.001 TRP B 635 HIS 0.003 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4230) covalent geometry : angle 0.46486 / 0.25 ( 5730) hydrogen bonds : bond 0.06385 / 4.17 ( 304) hydrogen bonds : angle 3.39011 / 2.44 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.186 Fit side-chains REVERT: A 819 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7438 (mp) REVERT: C 819 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7259 (mp) REVERT: D 833 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7141 (tm) outliers start: 9 outliers final: 1 residues processed: 77 average time/residue: 0.4422 time to fit residues: 35.4696 Evaluate side-chains 77 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 chunk 6 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 621 GLN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122523 restraints weight = 4446.114| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.51 r_work: 0.3213 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4230 Z= 0.123 Angle : 0.433 4.972 5730 Z= 0.233 Chirality : 0.034 0.125 678 Planarity : 0.004 0.033 654 Dihedral : 14.234 87.816 822 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.79 % Allowed : 10.41 % Favored : 86.80 % 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: 2.63 (0.38), residues: 496 helix: 2.61 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.89 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 582 TYR 0.004 0.001 TYR B 646 PHE 0.011 0.001 PHE A 627 TRP 0.009 0.001 TRP B 635 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4230) covalent geometry : angle 0.43338 / 0.23 ( 5730) hydrogen bonds : bond 0.05488 / 3.56 ( 304) hydrogen bonds : angle 3.22922 / 2.32 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.135 Fit side-chains REVERT: A 819 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7290 (mp) REVERT: C 819 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7052 (mp) REVERT: D 604 LYS cc_start: 0.8043 (mttp) cc_final: 0.7787 (mttm) REVERT: D 833 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6970 (tm) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 0.4369 time to fit residues: 35.5388 Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 621 GLN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120584 restraints weight = 4409.303| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.44 r_work: 0.3210 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4230 Z= 0.154 Angle : 0.472 5.272 5730 Z= 0.253 Chirality : 0.035 0.130 678 Planarity : 0.004 0.033 654 Dihedral : 14.714 88.848 822 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.05 % Allowed : 10.41 % Favored : 86.55 % 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: 2.52 (0.38), residues: 496 helix: 2.53 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.94 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 582 TYR 0.005 0.001 TYR D 646 PHE 0.012 0.002 PHE C 639 TRP 0.011 0.001 TRP D 635 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4230) covalent geometry : angle 0.47249 / 0.25 ( 5730) hydrogen bonds : bond 0.06231 / 4.06 ( 304) hydrogen bonds : angle 3.30125 / 2.38 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.100 Fit side-chains REVERT: A 819 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7392 (mp) REVERT: C 819 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7149 (mp) REVERT: D 604 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: D 833 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7074 (tm) outliers start: 12 outliers final: 4 residues processed: 80 average time/residue: 0.4266 time to fit residues: 35.5794 Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 621 GLN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121152 restraints weight = 4546.864| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.54 r_work: 0.3176 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4230 Z= 0.139 Angle : 0.458 5.155 5730 Z= 0.243 Chirality : 0.035 0.127 678 Planarity : 0.004 0.034 654 Dihedral : 14.595 89.063 822 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.79 % Allowed : 10.66 % Favored : 86.55 % 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: 2.67 (0.38), residues: 496 helix: 2.65 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.93 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 582 TYR 0.005 0.001 TYR B 646 PHE 0.012 0.001 PHE A 639 TRP 0.010 0.001 TRP D 635 HIS 0.002 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4230) covalent geometry : angle 0.45816 / 0.24 ( 5730) hydrogen bonds : bond 0.05818 / 3.78 ( 304) hydrogen bonds : angle 3.22844 / 2.33 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.090 Fit side-chains REVERT: A 819 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7285 (mp) REVERT: C 819 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7092 (mp) REVERT: D 833 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7034 (tm) outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 0.3864 time to fit residues: 31.7994 Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 616 ASN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121688 restraints weight = 4572.439| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.49 r_work: 0.3226 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4230 Z= 0.123 Angle : 0.442 5.508 5730 Z= 0.234 Chirality : 0.034 0.124 678 Planarity : 0.004 0.033 654 Dihedral : 14.416 88.654 822 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.54 % Allowed : 11.17 % Favored : 86.29 % 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: 2.94 (0.38), residues: 496 helix: 2.85 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -2.17 (0.57), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 582 TYR 0.004 0.001 TYR B 646 PHE 0.012 0.001 PHE A 639 TRP 0.010 0.001 TRP D 635 HIS 0.002 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4230) covalent geometry : angle 0.44225 / 0.23 ( 5730) hydrogen bonds : bond 0.05380 / 3.49 ( 304) hydrogen bonds : angle 3.14597 / 2.26 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.145 Fit side-chains REVERT: A 819 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7490 (mp) REVERT: D 833 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7107 (tm) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.4039 time to fit residues: 33.2502 Evaluate side-chains 81 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121415 restraints weight = 4451.451| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.51 r_work: 0.3194 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4230 Z= 0.144 Angle : 0.475 6.555 5730 Z= 0.250 Chirality : 0.035 0.130 678 Planarity : 0.004 0.033 654 Dihedral : 14.813 89.070 822 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.79 % Allowed : 11.42 % Favored : 85.79 % 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: 2.79 (0.37), residues: 496 helix: 2.74 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.93 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 582 TYR 0.005 0.001 TYR D 646 PHE 0.012 0.001 PHE C 639 TRP 0.010 0.001 TRP D 635 HIS 0.002 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4230) covalent geometry : angle 0.47513 / 0.25 ( 5730) hydrogen bonds : bond 0.05975 / 3.90 ( 304) hydrogen bonds : angle 3.23782 / 2.34 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.145 Fit side-chains REVERT: A 819 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7286 (mp) REVERT: D 833 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7011 (tm) outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 0.4016 time to fit residues: 33.4869 Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121760 restraints weight = 4478.504| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.53 r_work: 0.3174 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4230 Z= 0.135 Angle : 0.467 7.431 5730 Z= 0.245 Chirality : 0.035 0.129 678 Planarity : 0.004 0.033 654 Dihedral : 14.750 89.172 822 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.54 % Allowed : 11.93 % Favored : 85.53 % 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: 2.90 (0.37), residues: 496 helix: 2.81 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -2.16 (0.57), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 582 TYR 0.005 0.001 TYR B 646 PHE 0.012 0.001 PHE C 639 TRP 0.010 0.001 TRP C 563 HIS 0.002 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4230) covalent geometry : angle 0.46725 / 0.24 ( 5730) hydrogen bonds : bond 0.05631 / 3.66 ( 304) hydrogen bonds : angle 3.18192 / 2.29 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.147 Fit side-chains REVERT: A 819 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7271 (mp) REVERT: D 833 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7068 (tm) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.3837 time to fit residues: 30.8287 Evaluate side-chains 81 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121187 restraints weight = 4403.690| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.49 r_work: 0.3211 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4230 Z= 0.145 Angle : 0.484 8.087 5730 Z= 0.252 Chirality : 0.035 0.131 678 Planarity : 0.004 0.033 654 Dihedral : 14.882 89.483 822 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.28 % Allowed : 11.93 % Favored : 85.79 % 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: 2.80 (0.37), residues: 496 helix: 2.67 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.77 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 582 TYR 0.005 0.001 TYR B 823 PHE 0.012 0.001 PHE A 639 TRP 0.011 0.001 TRP A 563 HIS 0.002 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 4230) covalent geometry : angle 0.48401 / 0.25 ( 5730) hydrogen bonds : bond 0.05972 / 3.89 ( 304) hydrogen bonds : angle 3.23812 / 2.34 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.096 Fit side-chains REVERT: A 819 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7281 (mp) REVERT: C 830 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7795 (mm) REVERT: D 833 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7146 (tm) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.4145 time to fit residues: 32.8107 Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121217 restraints weight = 4421.367| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.50 r_work: 0.3214 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4230 Z= 0.142 Angle : 0.479 8.144 5730 Z= 0.250 Chirality : 0.035 0.131 678 Planarity : 0.004 0.033 654 Dihedral : 14.745 89.604 822 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.28 % Allowed : 11.68 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.37), residues: 496 helix: 2.78 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.97 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 582 TYR 0.006 0.001 TYR B 823 PHE 0.013 0.001 PHE A 639 TRP 0.010 0.001 TRP C 563 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4230) covalent geometry : angle 0.47905 / 0.25 ( 5730) hydrogen bonds : bond 0.05833 / 3.80 ( 304) hydrogen bonds : angle 3.21449 / 2.32 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.38 seconds wall clock time: 26 minutes 14.31 seconds (1574.31 seconds total)