Starting phenix.real_space_refine on Fri Aug 22 19:59:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmf_22257/08_2025/6xmf_22257.cif" } resolution = 3.1 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= 0.005 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 Zn 1 6.06 5 P 109 5.49 5 S 11 5.16 5 C 4235 2.51 5 N 1381 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7382 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5054 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 38, 'TRANS': 588} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'HIS:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2327 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 46} Link IDs: {'rna2p': 13, 'rna3p': 95} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4607 SG CYS A 711 52.215 79.966 49.609 1.00 49.88 S ATOM 4627 SG CYS A 714 51.876 82.146 46.526 1.00 58.23 S ATOM 4815 SG CYS A 735 55.331 81.541 48.049 1.00 66.85 S ATOM 4834 SG CYS A 738 52.449 83.643 49.885 1.00 68.17 S Time building chain proxies: 1.47, per 1000 atoms: 0.20 Number of scatterers: 7382 At special positions: 0 Unit cell: (84, 93.45, 132.3, 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) Zn 1 29.99 S 11 16.00 P 109 15.00 O 1645 8.00 N 1381 7.00 C 4235 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 292.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 711 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 738 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 735 " Number of angles added : 6 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 51.2% alpha, 5.9% beta 30 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.864A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 65 " --> pdb=" O CYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.756A pdb=" N PHE A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.758A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.642A pdb=" N SER A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 4.052A pdb=" N ASP A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.708A pdb=" N TRP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.812A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.873A pdb=" N LYS A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.781A pdb=" N LYS A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.810A pdb=" N ARG A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.562A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.593A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.745A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.729A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.506A pdb=" N GLU A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 647 removed outlier: 3.750A pdb=" N VAL A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 4.187A pdb=" N GLU A 666 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.552A pdb=" N PHE A 678 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.531A pdb=" N ILE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 3.909A pdb=" N ARG A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.829A pdb=" N TRP A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.850A pdb=" N PHE A 533 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 521 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 519 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 510 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 652 " --> pdb=" O VAL A 700 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 990 1.32 - 1.44: 2756 1.44 - 1.56: 3793 1.56 - 1.69: 215 1.69 - 1.81: 16 Bond restraints: 7770 Sorted by residual: bond pdb=" N ASP A 617 " pdb=" CA ASP A 617 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.16e-02 7.43e+03 1.29e+01 bond pdb=" C ASP A 617 " pdb=" O ASP A 617 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.16e-02 7.43e+03 1.20e+01 bond pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.61e-02 3.86e+03 7.18e+00 bond pdb=" CA LEU A 618 " pdb=" C LEU A 618 " ideal model delta sigma weight residual 1.526 1.538 -0.012 9.70e-03 1.06e+04 1.45e+00 bond pdb=" C3' G C 74 " pdb=" O3' G C 74 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.40e+00 ... (remaining 7765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 10729 1.48 - 2.95: 219 2.95 - 4.43: 51 4.43 - 5.90: 12 5.90 - 7.38: 4 Bond angle restraints: 11015 Sorted by residual: angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" CB PRO A 229 " ideal model delta sigma weight residual 103.00 110.38 -7.38 1.10e+00 8.26e-01 4.50e+01 angle pdb=" N ILE A 537 " pdb=" CA ILE A 537 " pdb=" C ILE A 537 " ideal model delta sigma weight residual 106.21 111.69 -5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" O ASP A 617 " pdb=" C ASP A 617 " pdb=" N LEU A 618 " ideal model delta sigma weight residual 122.08 117.60 4.48 1.07e+00 8.73e-01 1.75e+01 angle pdb=" CA LEU A 618 " pdb=" C LEU A 618 " pdb=" O LEU A 618 " ideal model delta sigma weight residual 121.86 116.85 5.01 1.39e+00 5.18e-01 1.30e+01 angle pdb=" C ASN A 239 " pdb=" N CYS A 240 " pdb=" CA CYS A 240 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.28e+01 ... (remaining 11010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 4504 35.82 - 71.64: 304 71.64 - 107.45: 48 107.45 - 143.27: 2 143.27 - 179.09: 5 Dihedral angle restraints: 4863 sinusoidal: 3031 harmonic: 1832 Sorted by residual: dihedral pdb=" O4' U C 55 " pdb=" C1' U C 55 " pdb=" N1 U C 55 " pdb=" C2 U C 55 " ideal model delta sinusoidal sigma weight residual 200.00 45.74 154.26 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual -128.00 51.09 -179.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" N PRO A 534 " pdb=" CA PRO A 534 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1122 0.046 - 0.093: 116 0.093 - 0.139: 19 0.139 - 0.186: 7 0.186 - 0.232: 1 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA PRO A 229 " pdb=" N PRO A 229 " pdb=" C PRO A 229 " pdb=" CB PRO A 229 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' A C 76 " pdb=" C4' A C 76 " pdb=" O3' A C 76 " pdb=" C2' A C 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C3' G C 74 " pdb=" C4' G C 74 " pdb=" O3' G C 74 " pdb=" C2' G C 74 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 1262 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 618 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU A 618 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A 618 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 619 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 616 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C PHE A 616 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE A 616 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 617 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 428 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 429 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.029 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1442 2.78 - 3.31: 6748 3.31 - 3.84: 13218 3.84 - 4.37: 16387 4.37 - 4.90: 24309 Nonbonded interactions: 62104 Sorted by model distance: nonbonded pdb=" OH TYR A 377 " pdb=" O2' A C 41 " model vdw 2.246 3.040 nonbonded pdb=" O2' A C 76 " pdb=" OP1 G C 77 " model vdw 2.250 3.040 nonbonded pdb=" O PRO A 77 " pdb=" OG SER A 132 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 427 " pdb=" OP2 C C 112 " model vdw 2.319 3.040 nonbonded pdb=" O2' U C 13 " pdb=" OP2 G C 22 " model vdw 2.323 3.040 ... (remaining 62099 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 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 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 0.043 7774 Z= 0.138 Angle : 0.570 8.386 11021 Z= 0.347 Chirality : 0.032 0.232 1265 Planarity : 0.004 0.051 1035 Dihedral : 21.158 179.092 3665 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: -1.78 (0.33), residues: 615 helix: -0.64 (0.31), residues: 283 sheet: -0.98 (0.67), residues: 62 loop : -1.73 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 130 TYR 0.010 0.001 TYR A 377 PHE 0.006 0.001 PHE A 108 TRP 0.008 0.001 TRP A 367 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7770) covalent geometry : angle 0.56181 (11015) hydrogen bonds : bond 0.27694 ( 293) hydrogen bonds : angle 9.03599 ( 758) metal coordination : bond 0.00911 ( 4) metal coordination : angle 4.24025 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7539 (ttm110) REVERT: A 177 ARG cc_start: 0.7060 (mtm180) cc_final: 0.6773 (mtm180) REVERT: A 214 ILE cc_start: 0.6881 (mt) cc_final: 0.6583 (mt) REVERT: A 675 ARG cc_start: 0.6911 (mtt90) cc_final: 0.6407 (mpt180) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1370 time to fit residues: 11.2719 Evaluate side-chains 44 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 572 HIS A 723 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.206518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159837 restraints weight = 8067.204| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.37 r_work: 0.3717 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7774 Z= 0.220 Angle : 0.708 10.971 11021 Z= 0.354 Chirality : 0.039 0.254 1265 Planarity : 0.006 0.051 1035 Dihedral : 22.310 173.325 2389 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.62 % Favored : 91.22 % Rotamer: Outliers : 1.59 % Allowed : 7.74 % Favored : 90.67 % 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 aren not related in a simple way. whole: -1.62 (0.33), residues: 615 helix: -0.24 (0.30), residues: 293 sheet: -1.55 (0.68), residues: 56 loop : -1.87 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 130 TYR 0.014 0.002 TYR A 175 PHE 0.017 0.002 PHE A 420 TRP 0.021 0.002 TRP A 632 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7770) covalent geometry : angle 0.69432 (11015) hydrogen bonds : bond 0.05771 ( 293) hydrogen bonds : angle 4.66638 ( 758) metal coordination : bond 0.00957 ( 4) metal coordination : angle 5.90874 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.233 Fit side-chains REVERT: A 214 ILE cc_start: 0.5971 (mt) cc_final: 0.5660 (mt) REVERT: A 745 ASP cc_start: 0.6417 (m-30) cc_final: 0.6208 (m-30) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.1342 time to fit residues: 9.6663 Evaluate side-chains 51 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.206300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160056 restraints weight = 7936.789| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.36 r_work: 0.3733 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7774 Z= 0.163 Angle : 0.618 9.456 11021 Z= 0.310 Chirality : 0.036 0.241 1265 Planarity : 0.005 0.052 1035 Dihedral : 22.279 175.099 2389 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.78 % Allowed : 10.52 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.34), residues: 615 helix: 0.23 (0.30), residues: 290 sheet: -1.62 (0.67), residues: 59 loop : -1.65 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.012 0.001 TYR A 175 PHE 0.015 0.002 PHE A 108 TRP 0.019 0.002 TRP A 82 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7770) covalent geometry : angle 0.60736 (11015) hydrogen bonds : bond 0.05041 ( 293) hydrogen bonds : angle 4.25110 ( 758) metal coordination : bond 0.00917 ( 4) metal coordination : angle 4.93953 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.226 Fit side-chains REVERT: A 214 ILE cc_start: 0.5957 (mt) cc_final: 0.5602 (mt) REVERT: A 388 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 745 ASP cc_start: 0.6855 (m-30) cc_final: 0.6648 (m-30) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.1277 time to fit residues: 9.7766 Evaluate side-chains 60 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.203081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154551 restraints weight = 8008.579| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.48 r_work: 0.3674 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7774 Z= 0.177 Angle : 0.626 9.664 11021 Z= 0.316 Chirality : 0.037 0.243 1265 Planarity : 0.005 0.051 1035 Dihedral : 22.250 174.439 2389 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.98 % Allowed : 13.69 % Favored : 83.33 % 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 aren not related in a simple way. whole: -1.07 (0.34), residues: 615 helix: 0.30 (0.31), residues: 292 sheet: -1.60 (0.75), residues: 50 loop : -1.62 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 675 TYR 0.011 0.002 TYR A 175 PHE 0.017 0.002 PHE A 420 TRP 0.021 0.002 TRP A 82 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7770) covalent geometry : angle 0.61392 (11015) hydrogen bonds : bond 0.04813 ( 293) hydrogen bonds : angle 4.10027 ( 758) metal coordination : bond 0.00841 ( 4) metal coordination : angle 5.30147 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.133 Fit side-chains REVERT: A 214 ILE cc_start: 0.5803 (mt) cc_final: 0.5444 (mt) REVERT: A 388 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8097 (mt) outliers start: 15 outliers final: 11 residues processed: 54 average time/residue: 0.1325 time to fit residues: 8.8262 Evaluate side-chains 56 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS A 440 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.205085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159517 restraints weight = 7893.210| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.32 r_work: 0.3703 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7774 Z= 0.145 Angle : 0.590 8.704 11021 Z= 0.298 Chirality : 0.035 0.239 1265 Planarity : 0.004 0.050 1035 Dihedral : 22.193 175.768 2389 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.35 % 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 aren not related in a simple way. whole: -0.95 (0.34), residues: 615 helix: 0.41 (0.30), residues: 293 sheet: -1.68 (0.74), residues: 50 loop : -1.56 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.014 0.002 PHE A 420 TRP 0.019 0.001 TRP A 82 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7770) covalent geometry : angle 0.57979 (11015) hydrogen bonds : bond 0.04555 ( 293) hydrogen bonds : angle 3.96579 ( 758) metal coordination : bond 0.00711 ( 4) metal coordination : angle 4.72912 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.244 Fit side-chains REVERT: A 388 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 752 LEU cc_start: 0.8486 (mt) cc_final: 0.8255 (mt) outliers start: 17 outliers final: 13 residues processed: 59 average time/residue: 0.1154 time to fit residues: 8.7267 Evaluate side-chains 61 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.205007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159441 restraints weight = 7818.801| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.31 r_work: 0.3694 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7774 Z= 0.153 Angle : 0.597 8.254 11021 Z= 0.301 Chirality : 0.036 0.240 1265 Planarity : 0.004 0.050 1035 Dihedral : 22.162 175.514 2389 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.57 % Allowed : 16.47 % Favored : 79.96 % 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 aren not related in a simple way. whole: -0.86 (0.34), residues: 615 helix: 0.47 (0.30), residues: 294 sheet: -1.77 (0.73), residues: 50 loop : -1.46 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.015 0.002 PHE A 420 TRP 0.018 0.001 TRP A 82 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7770) covalent geometry : angle 0.58781 (11015) hydrogen bonds : bond 0.04500 ( 293) hydrogen bonds : angle 3.90546 ( 758) metal coordination : bond 0.00648 ( 4) metal coordination : angle 4.54267 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.237 Fit side-chains REVERT: A 92 LEU cc_start: 0.7858 (mt) cc_final: 0.7395 (mt) REVERT: A 388 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8081 (mt) outliers start: 18 outliers final: 15 residues processed: 57 average time/residue: 0.1321 time to fit residues: 9.4353 Evaluate side-chains 61 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.202671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150219 restraints weight = 7974.297| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.45 r_work: 0.3705 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7774 Z= 0.174 Angle : 0.614 8.420 11021 Z= 0.310 Chirality : 0.037 0.241 1265 Planarity : 0.005 0.050 1035 Dihedral : 22.172 175.365 2389 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.17 % Allowed : 16.07 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.34), residues: 615 helix: 0.36 (0.30), residues: 303 sheet: -1.77 (0.73), residues: 50 loop : -1.62 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.017 0.002 PHE A 420 TRP 0.019 0.002 TRP A 82 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7770) covalent geometry : angle 0.60350 (11015) hydrogen bonds : bond 0.04581 ( 293) hydrogen bonds : angle 3.96688 ( 758) metal coordination : bond 0.00627 ( 4) metal coordination : angle 4.80162 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 388 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 630 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7031 (ptt180) REVERT: A 752 LEU cc_start: 0.8559 (mt) cc_final: 0.8298 (mt) outliers start: 21 outliers final: 14 residues processed: 62 average time/residue: 0.1359 time to fit residues: 10.5071 Evaluate side-chains 63 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.205777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156841 restraints weight = 7897.838| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.28 r_work: 0.3732 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7774 Z= 0.137 Angle : 0.595 9.077 11021 Z= 0.300 Chirality : 0.035 0.240 1265 Planarity : 0.004 0.050 1035 Dihedral : 22.115 176.240 2389 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.97 % Allowed : 16.07 % Favored : 79.96 % 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 aren not related in a simple way. whole: -0.76 (0.34), residues: 615 helix: 0.64 (0.30), residues: 300 sheet: -1.83 (0.72), residues: 50 loop : -1.56 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.014 0.002 PHE A 420 TRP 0.018 0.001 TRP A 82 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7770) covalent geometry : angle 0.58683 (11015) hydrogen bonds : bond 0.04369 ( 293) hydrogen bonds : angle 3.83741 ( 758) metal coordination : bond 0.00620 ( 4) metal coordination : angle 4.36827 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8039 (mt) cc_final: 0.7468 (mt) REVERT: A 388 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 483 GLN cc_start: 0.8191 (tt0) cc_final: 0.7973 (tt0) REVERT: A 752 LEU cc_start: 0.8554 (mt) cc_final: 0.8323 (mt) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.1430 time to fit residues: 11.0822 Evaluate side-chains 64 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.205915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153915 restraints weight = 7908.376| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.45 r_work: 0.3719 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7774 Z= 0.133 Angle : 0.595 9.485 11021 Z= 0.299 Chirality : 0.035 0.239 1265 Planarity : 0.005 0.051 1035 Dihedral : 22.064 176.251 2389 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.57 % Allowed : 15.87 % Favored : 80.56 % 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 aren not related in a simple way. whole: -0.62 (0.34), residues: 615 helix: 0.74 (0.30), residues: 298 sheet: -1.83 (0.71), residues: 50 loop : -1.44 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 130 TYR 0.011 0.002 TYR A 175 PHE 0.013 0.002 PHE A 108 TRP 0.018 0.001 TRP A 82 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7770) covalent geometry : angle 0.58701 (11015) hydrogen bonds : bond 0.04331 ( 293) hydrogen bonds : angle 3.79280 ( 758) metal coordination : bond 0.00597 ( 4) metal coordination : angle 4.18685 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8115 (mt) cc_final: 0.7540 (mt) REVERT: A 388 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 483 GLN cc_start: 0.8193 (tt0) cc_final: 0.7924 (tt0) REVERT: A 752 LEU cc_start: 0.8528 (mt) cc_final: 0.8275 (mt) outliers start: 18 outliers final: 15 residues processed: 58 average time/residue: 0.1244 time to fit residues: 8.9477 Evaluate side-chains 64 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.203338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151086 restraints weight = 7889.370| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.44 r_work: 0.3695 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7774 Z= 0.173 Angle : 0.622 9.951 11021 Z= 0.311 Chirality : 0.036 0.240 1265 Planarity : 0.005 0.053 1035 Dihedral : 22.075 175.409 2389 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.17 % Allowed : 16.47 % Favored : 80.36 % 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 aren not related in a simple way. whole: -0.73 (0.34), residues: 615 helix: 0.66 (0.30), residues: 298 sheet: -1.82 (0.72), residues: 50 loop : -1.51 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 130 TYR 0.011 0.002 TYR A 175 PHE 0.016 0.002 PHE A 420 TRP 0.018 0.002 TRP A 82 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7770) covalent geometry : angle 0.61318 (11015) hydrogen bonds : bond 0.04487 ( 293) hydrogen bonds : angle 3.87285 ( 758) metal coordination : bond 0.00605 ( 4) metal coordination : angle 4.56724 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8176 (mt) cc_final: 0.7591 (mt) REVERT: A 388 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8162 (mt) outliers start: 16 outliers final: 14 residues processed: 54 average time/residue: 0.1308 time to fit residues: 8.9217 Evaluate side-chains 58 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.206704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154958 restraints weight = 7937.626| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.45 r_work: 0.3758 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7774 Z= 0.124 Angle : 0.587 10.243 11021 Z= 0.294 Chirality : 0.034 0.239 1265 Planarity : 0.004 0.054 1035 Dihedral : 22.015 176.507 2389 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.98 % Allowed : 17.06 % Favored : 79.96 % 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 aren not related in a simple way. whole: -0.52 (0.34), residues: 615 helix: 0.88 (0.30), residues: 298 sheet: -1.89 (0.71), residues: 50 loop : -1.43 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 130 TYR 0.011 0.001 TYR A 175 PHE 0.013 0.002 PHE A 108 TRP 0.019 0.001 TRP A 82 HIS 0.003 0.001 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7770) covalent geometry : angle 0.57943 (11015) hydrogen bonds : bond 0.04280 ( 293) hydrogen bonds : angle 3.75131 ( 758) metal coordination : bond 0.00569 ( 4) metal coordination : angle 3.98937 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.89 seconds wall clock time: 34 minutes 30.33 seconds (2070.33 seconds total)