Starting phenix.real_space_refine on Tue Aug 4 13:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.cif Found real_map, /net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28xa_56932/08_2026/28xa_56932.map" } resolution = 4.86 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: 3 Type Number sf(0) Gaussians C 1960 2.51 5 N 649 2.21 5 O 650 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3259 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1106 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 689 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'HIS:plan': 6, 'TRP:plan': 2, 'GLU:plan': 17, 'GLN:plan1': 9, 'ASP:plan': 9, 'TYR:plan': 11, 'PHE:plan': 11, 'ARG:plan': 13, 'ASN:plan1': 6, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 411 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 1898 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1568 Unresolved non-hydrogen dihedrals: 1050 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'TYR:plan': 18, 'GLN:plan1': 20, 'GLU:plan': 22, 'ASP:plan': 18, 'ARG:plan': 14, 'PHE:plan': 22, 'HIS:plan': 16, 'ASN:plan1': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 684 Chain: "C" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 230 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'PHE:plan': 2, 'ASP:plan': 10, 'TRP:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.17, per 1000 atoms: 0.36 Number of scatterers: 3259 At special positions: 0 Unit cell: (62.338, 91.312, 108.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 650 8.00 N 649 7.00 C 1960 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: 0.31 Conformation dependent library (CDL) restraints added in 180.5 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 77.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.555A pdb=" N LYS A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 614 Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'A' and resid 636 through 653 removed outlier: 3.820A pdb=" N GLN A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 674 Processing helix chain 'A' and resid 675 through 686 Processing helix chain 'A' and resid 687 through 693 Processing helix chain 'A' and resid 693 through 709 Processing helix chain 'A' and resid 710 through 720 removed outlier: 3.779A pdb=" N PHE A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 748 removed outlier: 4.057A pdb=" N LEU A 728 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 Processing helix chain 'A' and resid 764 through 774 removed outlier: 3.709A pdb=" N ALA A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 21 through 30 removed outlier: 3.530A pdb=" N GLU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.625A pdb=" N MET B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 62 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 104 through 130 removed outlier: 3.571A pdb=" N VAL B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 3.656A pdb=" N LYS B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.517A pdb=" N SER B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS B 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 165 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 removed outlier: 3.762A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 198 removed outlier: 4.223A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.124A pdb=" N PHE B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 262 removed outlier: 3.657A pdb=" N TYR B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 274 removed outlier: 3.586A pdb=" N LEU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.675A pdb=" N ALA B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 309 through 316 removed outlier: 4.181A pdb=" N ILE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 334 removed outlier: 4.172A pdb=" N ILE B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.600A pdb=" N HIS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 752 through 753 Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.748A pdb=" N VAL B 385 " --> pdb=" O TYR B 376 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 376 " --> pdb=" O VAL B 385 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 960 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: 0.33 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 650 1.28 - 1.35: 641 1.35 - 1.41: 3 1.41 - 1.48: 681 1.48 - 1.54: 1296 Bond restraints: 3271 Sorted by residual: bond pdb=" CB PRO A 722 " pdb=" CG PRO A 722 " ideal model delta sigma weight residual 1.492 1.401 0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CA LEU A 700 " pdb=" C LEU A 700 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.29e-02 6.01e+03 3.05e+00 bond pdb=" C VAL A 696 " pdb=" O VAL A 696 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.29e-02 6.01e+03 2.64e+00 bond pdb=" C THR A 626 " pdb=" N HIS A 627 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.31e-02 5.83e+03 2.64e+00 bond pdb=" N LEU A 702 " pdb=" CA LEU A 702 " ideal model delta sigma weight residual 1.459 1.440 0.020 1.21e-02 6.83e+03 2.62e+00 ... (remaining 3266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 3950 1.38 - 2.76: 522 2.76 - 4.14: 67 4.14 - 5.52: 27 5.52 - 6.90: 4 Bond angle restraints: 4570 Sorted by residual: angle pdb=" N PHE B 226 " pdb=" CA PHE B 226 " pdb=" C PHE B 226 " ideal model delta sigma weight residual 111.71 116.70 -4.99 1.15e+00 7.56e-01 1.88e+01 angle pdb=" N PHE A 714 " pdb=" CA PHE A 714 " pdb=" C PHE A 714 " ideal model delta sigma weight residual 111.07 115.18 -4.11 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N ARG B 116 " pdb=" CA ARG B 116 " pdb=" C ARG B 116 " ideal model delta sigma weight residual 111.07 114.85 -3.78 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N GLU B 353 " pdb=" CA GLU B 353 " pdb=" C GLU B 353 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N MET B 168 " pdb=" CA MET B 168 " pdb=" C MET B 168 " ideal model delta sigma weight residual 111.03 114.52 -3.49 1.11e+00 8.12e-01 9.91e+00 ... (remaining 4565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1944 17.95 - 35.89: 5 35.89 - 53.84: 0 53.84 - 71.78: 0 71.78 - 89.73: 1 Dihedral angle restraints: 1950 sinusoidal: 55 harmonic: 1895 Sorted by residual: dihedral pdb=" CA ASP A 636 " pdb=" C ASP A 636 " pdb=" N HIS A 637 " pdb=" CA HIS A 637 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ASP B 21 " pdb=" C ASP B 21 " pdb=" N GLY B 22 " pdb=" CA GLY B 22 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ILE B 310 " pdb=" C ILE B 310 " pdb=" N PHE B 311 " pdb=" CA PHE B 311 " ideal model delta harmonic sigma weight residual 180.00 165.65 14.35 0 5.00e+00 4.00e-02 8.23e+00 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 384 0.031 - 0.063: 159 0.063 - 0.094: 67 0.094 - 0.126: 11 0.126 - 0.157: 5 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA PRO A 694 " pdb=" N PRO A 694 " pdb=" C PRO A 694 " pdb=" CB PRO A 694 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE A 788 " pdb=" N ILE A 788 " pdb=" C ILE A 788 " pdb=" CB ILE A 788 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 377 " pdb=" N ILE B 377 " pdb=" C ILE B 377 " pdb=" CB ILE B 377 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 623 not shown) Planarity restraints: 661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 696 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C VAL A 696 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL A 696 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA A 697 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 640 " -0.021 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE A 640 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE A 640 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 641 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 756 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C TYR A 756 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 756 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 757 " -0.016 2.00e-02 2.50e+03 ... (remaining 658 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2345 3.04 - 3.51: 3793 3.51 - 3.97: 4343 3.97 - 4.44: 5389 4.44 - 4.90: 6809 Nonbonded interactions: 22679 Sorted by model distance: nonbonded pdb=" O LEU C 60 " pdb=" O GLY C 64 " model vdw 2.581 3.040 nonbonded pdb=" N SER B 132 " pdb=" O SER B 132 " model vdw 2.583 2.496 nonbonded pdb=" N ASP B 356 " pdb=" O ASP B 356 " model vdw 2.611 2.496 nonbonded pdb=" N LYS B 133 " pdb=" O LYS B 133 " model vdw 2.625 2.496 nonbonded pdb=" N ARG A 749 " pdb=" O ARG A 749 " model vdw 2.638 2.496 ... (remaining 22674 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.680 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.700 Find NCS groups from input model: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.007 0.091 3271 Z= 0.440 Angle : 1.038 6.900 4570 Z= 0.720 Chirality : 0.040 0.157 626 Planarity : 0.008 0.042 661 Dihedral : 4.900 89.725 698 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.82 (0.33), residues: 637 helix: 0.61 (0.23), residues: 460 sheet: -2.83 (1.46), residues: 10 loop : 1.05 (0.54), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.44 ( 3271) covalent geometry : angle 1.03787 / 0.72 ( 4570) hydrogen bonds : bond 0.21122 / 15.96 ( 324) hydrogen bonds : angle 7.84563 / 6.11 ( 960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0191 time to fit residues: 0.7895 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049648 restraints weight = 34660.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049648 restraints weight = 34648.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049648 restraints weight = 34648.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049648 restraints weight = 34648.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049648 restraints weight = 34648.079| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3271 Z= 0.372 Angle : 0.619 6.363 4570 Z= 0.416 Chirality : 0.036 0.124 626 Planarity : 0.005 0.047 661 Dihedral : 6.041 82.825 644 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.73 (0.34), residues: 637 helix: 0.48 (0.23), residues: 450 sheet: -1.03 (1.61), residues: 10 loop : 1.05 (0.55), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.37 ( 3271) covalent geometry : angle 0.61883 / 0.42 ( 4570) hydrogen bonds : bond 0.06983 / 5.25 ( 324) hydrogen bonds : angle 5.65718 / 4.48 ( 960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.140 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0168 time to fit residues: 0.6623 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 45 optimal weight: 0.0170 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050388 restraints weight = 34321.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050388 restraints weight = 34421.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050388 restraints weight = 34421.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050388 restraints weight = 34421.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050388 restraints weight = 34421.956| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3271 Z= 0.203 Angle : 0.485 6.045 4570 Z= 0.304 Chirality : 0.035 0.120 626 Planarity : 0.004 0.039 661 Dihedral : 5.386 71.249 644 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 1.08 (0.34), residues: 637 helix: 0.92 (0.24), residues: 459 sheet: -0.48 (1.84), residues: 10 loop : 0.59 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.20 ( 3271) covalent geometry : angle 0.48522 / 0.30 ( 4570) hydrogen bonds : bond 0.05065 / 3.81 ( 324) hydrogen bonds : angle 4.83360 / 3.84 ( 960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0150 time to fit residues: 0.6001 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 57 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048472 restraints weight = 35516.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048472 restraints weight = 35210.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048472 restraints weight = 35207.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048472 restraints weight = 35207.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048472 restraints weight = 35207.741| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3271 Z= 0.246 Angle : 0.530 5.630 4570 Z= 0.339 Chirality : 0.035 0.115 626 Planarity : 0.004 0.039 661 Dihedral : 5.749 55.981 644 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.40 (0.33), residues: 637 helix: 0.42 (0.24), residues: 460 sheet: None (None), residues: 0 loop : 0.21 (0.52), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.25 ( 3271) covalent geometry : angle 0.52964 / 0.34 ( 4570) hydrogen bonds : bond 0.05694 / 4.29 ( 324) hydrogen bonds : angle 5.20216 / 4.14 ( 960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0135 time to fit residues: 0.5567 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.046332 restraints weight = 34690.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046360 restraints weight = 34264.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046424 restraints weight = 34153.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046424 restraints weight = 33808.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046424 restraints weight = 33808.225| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3271 Z= 0.307 Angle : 0.578 5.185 4570 Z= 0.384 Chirality : 0.036 0.123 626 Planarity : 0.004 0.040 661 Dihedral : 6.194 51.614 644 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.33 (0.33), residues: 637 helix: -0.06 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -0.22 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.31 ( 3271) covalent geometry : angle 0.57842 / 0.38 ( 4570) hydrogen bonds : bond 0.06448 / 4.87 ( 324) hydrogen bonds : angle 5.65906 / 4.50 ( 960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0161 time to fit residues: 0.6862 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 overall best weight: 3.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.048087 restraints weight = 33620.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048144 restraints weight = 33125.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048144 restraints weight = 32695.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048249 restraints weight = 32695.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048250 restraints weight = 32228.116| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3271 Z= 0.193 Angle : 0.474 5.332 4570 Z= 0.297 Chirality : 0.035 0.124 626 Planarity : 0.003 0.037 661 Dihedral : 5.259 43.799 644 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.34 (0.33), residues: 637 helix: 0.58 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.45 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.19 ( 3271) covalent geometry : angle 0.47430 / 0.30 ( 4570) hydrogen bonds : bond 0.04838 / 3.62 ( 324) hydrogen bonds : angle 4.92237 / 3.91 ( 960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0153 time to fit residues: 0.6068 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043587 restraints weight = 32785.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 12)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043586 restraints weight = 32804.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043586 restraints weight = 32811.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043586 restraints weight = 32811.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043586 restraints weight = 32811.373| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3271 Z= 0.354 Angle : 0.611 5.229 4570 Z= 0.411 Chirality : 0.036 0.124 626 Planarity : 0.004 0.037 661 Dihedral : 6.319 41.515 644 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.98 (0.32), residues: 637 helix: -0.37 (0.23), residues: 455 sheet: None (None), residues: 0 loop : -1.00 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.35 ( 3271) covalent geometry : angle 0.61132 / 0.41 ( 4570) hydrogen bonds : bond 0.06961 / 5.25 ( 324) hydrogen bonds : angle 6.02164 / 4.79 ( 960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0121 time to fit residues: 0.5378 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.047545 restraints weight = 34927.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047670 restraints weight = 34523.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047670 restraints weight = 33863.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047670 restraints weight = 33863.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047670 restraints weight = 33863.133| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3271 Z= 0.180 Angle : 0.469 5.336 4570 Z= 0.292 Chirality : 0.034 0.119 626 Planarity : 0.003 0.036 661 Dihedral : 5.226 36.631 644 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.00 (0.33), residues: 637 helix: 0.42 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -0.85 (0.48), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.18 ( 3271) covalent geometry : angle 0.46860 / 0.29 ( 4570) hydrogen bonds : bond 0.04760 / 3.56 ( 324) hydrogen bonds : angle 4.99604 / 3.97 ( 960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0101 time to fit residues: 0.3963 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.046903 restraints weight = 34144.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046945 restraints weight = 33602.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046945 restraints weight = 33253.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046945 restraints weight = 33253.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046945 restraints weight = 33253.887| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3271 Z= 0.225 Angle : 0.491 5.276 4570 Z= 0.315 Chirality : 0.035 0.117 626 Planarity : 0.003 0.035 661 Dihedral : 5.277 32.813 644 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.03 (0.33), residues: 637 helix: 0.40 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -0.86 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.23 ( 3271) covalent geometry : angle 0.49091 / 0.31 ( 4570) hydrogen bonds : bond 0.05111 / 3.83 ( 324) hydrogen bonds : angle 5.15705 / 4.09 ( 960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0103 time to fit residues: 0.4023 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 32 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 49 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049183 restraints weight = 33881.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049198 restraints weight = 33298.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049198 restraints weight = 33195.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049198 restraints weight = 33195.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049198 restraints weight = 33194.911| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3271 Z= 0.130 Angle : 0.419 5.295 4570 Z= 0.252 Chirality : 0.034 0.122 626 Planarity : 0.003 0.032 661 Dihedral : 4.485 29.526 644 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.98 (0.35), residues: 637 helix: 1.15 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.13 ( 3271) covalent geometry : angle 0.41923 / 0.25 ( 4570) hydrogen bonds : bond 0.03829 / 2.85 ( 324) hydrogen bonds : angle 4.39717 / 3.48 ( 960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.154 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0157 time to fit residues: 0.6633 Evaluate side-chains 16 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 0.0370 chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048481 restraints weight = 35330.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048481 restraints weight = 34524.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048481 restraints weight = 34524.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048481 restraints weight = 34524.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048481 restraints weight = 34524.202| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3271 Z= 0.160 Angle : 0.434 5.284 4570 Z= 0.267 Chirality : 0.034 0.119 626 Planarity : 0.003 0.031 661 Dihedral : 4.518 27.487 644 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 1.01 (0.35), residues: 637 helix: 1.21 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -0.63 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 596 PHE 0.000 0.000 PHE A 598 TRP 0.000 0.000 TRP A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.16 ( 3271) covalent geometry : angle 0.43433 / 0.27 ( 4570) hydrogen bonds : bond 0.04136 / 3.09 ( 324) hydrogen bonds : angle 4.48327 / 3.53 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 593.88 seconds wall clock time: 10 minutes 48.81 seconds (648.81 seconds total)