Starting phenix.real_space_refine on Fri Sep 11 04:08:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_22257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xmf_22257/09_2026/6xmf_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 1.67, per 1000 atoms: 0.23 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: 0.62 Conformation dependent library (CDL) restraints added in 314.5 milliseconds 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: 0.93 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: 1.34 Time building geometry restraints manager: 0.84 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=" C3' G C 74 " pdb=" O3' G C 74 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.21e+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 ... (remaining 7765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 10430 1.48 - 2.95: 453 2.95 - 4.43: 99 4.43 - 5.90: 29 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=" C3' G C 74 " pdb=" O3' G C 74 " pdb=" P A C 75 " ideal model delta sigma weight residual 119.70 125.41 -5.71 1.20e+00 6.94e-01 2.26e+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 ... (remaining 11010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.76: 4178 33.76 - 67.53: 267 67.53 - 101.29: 24 101.29 - 135.05: 1 135.05 - 168.82: 3 Dihedral angle restraints: 4473 sinusoidal: 2641 harmonic: 1832 Sorted by residual: dihedral pdb=" C4' A C 14 " pdb=" C3' A C 14 " pdb=" C2' A C 14 " pdb=" C1' A C 14 " ideal model delta sinusoidal sigma weight residual 36.35 -36.60 72.94 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' A C 54 " pdb=" C3' A C 54 " pdb=" C2' A C 54 " pdb=" C1' A C 54 " ideal model delta sinusoidal sigma weight residual 36.34 -36.00 72.34 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' U C 106 " pdb=" C3' U C 106 " pdb=" C2' U C 106 " pdb=" C1' U C 106 " ideal model delta sinusoidal sigma weight residual 36.35 -35.95 72.30 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 4470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1087 0.078 - 0.155: 40 0.155 - 0.233: 49 0.233 - 0.310: 87 0.310 - 0.388: 2 Chirality restraints: 1265 Sorted by residual: chirality pdb=" P A C 75 " pdb=" OP1 A C 75 " pdb=" OP2 A C 75 " pdb=" O5' A C 75 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" P A C 30 " pdb=" OP1 A C 30 " pdb=" OP2 A C 30 " pdb=" O5' A C 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C2' G C 74 " pdb=" C3' G C 74 " pdb=" O2' G C 74 " pdb=" C1' G C 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (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: 0.630 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7774 Z= 0.153 Angle : 0.763 8.386 11021 Z= 0.397 Chirality : 0.086 0.388 1265 Planarity : 0.004 0.051 1035 Dihedral : 18.609 168.816 3275 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 are 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/Z covalent geometry : bond 0.00265 / 0.15 ( 7770) covalent geometry : angle 0.75672 / 0.40 (11015) hydrogen bonds : bond 0.27694 / 18.91 ( 293) hydrogen bonds : angle 9.03599 / 6.34 ( 758) metal coordination : bond 0.00911 / 0.44 ( 4) metal coordination : angle 4.24025 / 2.87 ( 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 : 0.226 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: 0.6912 (mtt90) cc_final: 0.6407 (mpt180) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1330 time to fit residues: 11.0690 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 : 0.221 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4498 r_free = 0.4498 target = 0.210058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164761 restraints weight = 8131.344| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.57 r_work: 0.3799 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7774 Z= 0.226 Angle : 1.063 20.973 11021 Z= 0.445 Chirality : 0.080 0.851 1265 Planarity : 0.005 0.050 1035 Dihedral : 17.265 178.062 1999 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.39 % Allowed : 7.74 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.33), residues: 615 helix: -0.20 (0.30), residues: 293 sheet: -1.31 (0.69), residues: 59 loop : -1.97 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 130 TYR 0.013 0.002 TYR A 175 PHE 0.017 0.002 PHE A 756 TRP 0.020 0.002 TRP A 632 HIS 0.006 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 7770) covalent geometry : angle 1.05452 / 0.44 (11015) hydrogen bonds : bond 0.06229 / 3.98 ( 293) hydrogen bonds : angle 4.62041 / 3.13 ( 758) metal coordination : bond 0.00905 / 0.56 ( 4) metal coordination : angle 5.90899 / 3.73 ( 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 65 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.196 Fit side-chains REVERT: A 214 ILE cc_start: 0.6033 (mt) cc_final: 0.5721 (mt) REVERT: A 745 ASP cc_start: 0.6558 (m-30) cc_final: 0.6330 (m-30) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1231 time to fit residues: 9.1436 Evaluate side-chains 50 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.208332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159759 restraints weight = 7929.966| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.26 r_work: 0.3797 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2842 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= 0.177 Angle : 0.863 9.825 11021 Z= 0.371 Chirality : 0.061 0.480 1265 Planarity : 0.005 0.051 1035 Dihedral : 17.745 173.504 1999 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.98 % Allowed : 10.71 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.34), residues: 615 helix: 0.22 (0.30), residues: 290 sheet: -1.60 (0.67), residues: 59 loop : -1.59 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.015 0.002 PHE A 420 TRP 0.019 0.002 TRP A 82 HIS 0.007 0.002 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 7770) covalent geometry : angle 0.85539 / 0.37 (11015) hydrogen bonds : bond 0.05480 / 3.52 ( 293) hydrogen bonds : angle 4.18609 / 2.86 ( 758) metal coordination : bond 0.00816 / 0.40 ( 4) metal coordination : angle 5.10087 / 3.15 ( 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 72 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.207 Fit side-chains REVERT: A 214 ILE cc_start: 0.6050 (mt) cc_final: 0.5686 (mt) REVERT: A 388 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 690 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 745 ASP cc_start: 0.6710 (m-30) cc_final: 0.6509 (m-30) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1459 time to fit residues: 11.5248 Evaluate side-chains 67 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.204216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152104 restraints weight = 8080.591| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.47 r_work: 0.3725 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3210 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= 0.184 Angle : 0.860 10.955 11021 Z= 0.370 Chirality : 0.061 0.463 1265 Planarity : 0.005 0.049 1035 Dihedral : 17.731 179.657 1999 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.18 % Allowed : 14.48 % 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 are not related in a simple way. whole: -1.05 (0.34), residues: 615 helix: 0.30 (0.30), residues: 292 sheet: -1.60 (0.74), residues: 50 loop : -1.61 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.016 0.002 PHE A 420 TRP 0.020 0.002 TRP A 82 HIS 0.006 0.002 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 7770) covalent geometry : angle 0.85204 / 0.37 (11015) hydrogen bonds : bond 0.05354 / 3.47 ( 293) hydrogen bonds : angle 4.06005 / 2.77 ( 758) metal coordination : bond 0.00781 / 0.38 ( 4) metal coordination : angle 5.15735 / 3.13 ( 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 66 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.244 Fit side-chains REVERT: A 92 LEU cc_start: 0.8223 (mt) cc_final: 0.7577 (mt) REVERT: A 214 ILE cc_start: 0.5828 (mt) cc_final: 0.5462 (mt) REVERT: A 388 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 690 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7178 (mt-10) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1288 time to fit residues: 9.5431 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** 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 = 0.4455 r_free = 0.4455 target = 0.206263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154830 restraints weight = 8069.535| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.49 r_work: 0.3770 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3344 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= 0.148 Angle : 0.803 9.527 11021 Z= 0.346 Chirality : 0.058 0.443 1265 Planarity : 0.004 0.050 1035 Dihedral : 17.643 176.091 1999 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.34), residues: 615 helix: 0.45 (0.31), residues: 295 sheet: -1.69 (0.74), residues: 50 loop : -1.45 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 130 TYR 0.012 0.002 TYR A 175 PHE 0.015 0.002 PHE A 108 TRP 0.018 0.001 TRP A 82 HIS 0.005 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7770) covalent geometry : angle 0.79631 / 0.35 (11015) hydrogen bonds : bond 0.05105 / 3.28 ( 293) hydrogen bonds : angle 3.84872 / 2.63 ( 758) metal coordination : bond 0.00630 / 0.31 ( 4) metal coordination : angle 4.40643 / 2.70 ( 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 71 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.158 Fit side-chains REVERT: A 92 LEU cc_start: 0.8175 (mt) cc_final: 0.7543 (mt) REVERT: A 366 TYR cc_start: 0.3683 (m-10) cc_final: 0.3256 (m-80) REVERT: A 388 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 483 GLN cc_start: 0.8277 (tt0) cc_final: 0.8007 (tt0) REVERT: A 690 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7210 (mt-10) outliers start: 15 outliers final: 12 residues processed: 62 average time/residue: 0.1094 time to fit residues: 8.5422 Evaluate side-chains 64 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 618 LEU 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: 2.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** 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 = 0.4427 r_free = 0.4427 target = 0.203032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152940 restraints weight = 7881.856| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.38 r_work: 0.3738 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7774 Z= 0.183 Angle : 0.832 9.650 11021 Z= 0.361 Chirality : 0.059 0.441 1265 Planarity : 0.005 0.049 1035 Dihedral : 17.597 177.809 1999 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % 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 are not related in a simple way. whole: -0.88 (0.34), residues: 615 helix: 0.43 (0.30), residues: 295 sheet: -1.72 (0.74), residues: 50 loop : -1.47 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 130 TYR 0.011 0.002 TYR A 175 PHE 0.017 0.002 PHE A 420 TRP 0.018 0.002 TRP A 82 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 7770) covalent geometry : angle 0.82533 / 0.36 (11015) hydrogen bonds : bond 0.05161 / 3.35 ( 293) hydrogen bonds : angle 3.89999 / 2.65 ( 758) metal coordination : bond 0.00644 / 0.32 ( 4) metal coordination : angle 4.71577 / 2.85 ( 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 68 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.219 Fit side-chains REVERT: A 92 LEU cc_start: 0.8172 (mt) cc_final: 0.7525 (mt) REVERT: A 388 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8123 (mt) REVERT: A 690 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7090 (mt-10) outliers start: 17 outliers final: 12 residues processed: 60 average time/residue: 0.1117 time to fit residues: 8.5283 Evaluate side-chains 59 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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 618 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: 0.8980 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** 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 = 0.4459 r_free = 0.4459 target = 0.206505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155281 restraints weight = 8055.305| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.48 r_work: 0.3759 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3509 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= 0.146 Angle : 0.805 9.551 11021 Z= 0.348 Chirality : 0.058 0.425 1265 Planarity : 0.004 0.052 1035 Dihedral : 17.562 176.952 1999 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.57 % Allowed : 15.28 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.34), residues: 615 helix: 0.59 (0.31), residues: 295 sheet: -1.78 (0.73), residues: 50 loop : -1.36 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 130 TYR 0.017 0.002 TYR A 393 PHE 0.014 0.002 PHE A 108 TRP 0.017 0.001 TRP A 82 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 7770) covalent geometry : angle 0.79919 / 0.35 (11015) hydrogen bonds : bond 0.05046 / 3.24 ( 293) hydrogen bonds : angle 3.80528 / 2.60 ( 758) metal coordination : bond 0.00601 / 0.29 ( 4) metal coordination : angle 4.28555 / 2.62 ( 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: 18 poor density : 52 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8206 (mt) cc_final: 0.7587 (mt) REVERT: A 388 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 630 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7032 (ptt180) REVERT: A 690 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7203 (mt-10) outliers start: 18 outliers final: 15 residues processed: 62 average time/residue: 0.1277 time to fit residues: 9.7830 Evaluate side-chains 66 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 618 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: 0.6980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.205995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156282 restraints weight = 7997.453| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.39 r_work: 0.3776 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3556 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= 0.140 Angle : 0.798 9.483 11021 Z= 0.344 Chirality : 0.057 0.420 1265 Planarity : 0.005 0.058 1035 Dihedral : 17.529 176.778 1999 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.97 % Allowed : 15.28 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.34), residues: 615 helix: 0.79 (0.31), residues: 293 sheet: -1.79 (0.72), residues: 50 loop : -1.33 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 130 TYR 0.012 0.001 TYR A 175 PHE 0.014 0.002 PHE A 108 TRP 0.017 0.001 TRP A 82 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7770) covalent geometry : angle 0.79286 / 0.34 (11015) hydrogen bonds : bond 0.04994 / 3.21 ( 293) hydrogen bonds : angle 3.74045 / 2.55 ( 758) metal coordination : bond 0.00556 / 0.27 ( 4) metal coordination : angle 4.02868 / 2.49 ( 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 70 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8238 (mt) cc_final: 0.7686 (mt) REVERT: A 202 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5513 (pm20) REVERT: A 388 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 483 GLN cc_start: 0.8220 (tt0) cc_final: 0.7952 (tt0) REVERT: A 630 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.7006 (ptt180) REVERT: A 690 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7188 (mt-10) outliers start: 20 outliers final: 14 residues processed: 61 average time/residue: 0.1207 time to fit residues: 9.2092 Evaluate side-chains 66 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 202 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.207118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155596 restraints weight = 7979.743| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.46 r_work: 0.3758 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3683 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= 0.159 Angle : 0.808 9.417 11021 Z= 0.349 Chirality : 0.058 0.406 1265 Planarity : 0.005 0.053 1035 Dihedral : 17.475 177.302 1999 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.77 % Allowed : 15.28 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.34), residues: 615 helix: 0.80 (0.31), residues: 293 sheet: -1.79 (0.73), residues: 50 loop : -1.36 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 130 TYR 0.014 0.002 TYR A 393 PHE 0.015 0.002 PHE A 420 TRP 0.017 0.001 TRP A 82 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 7770) covalent geometry : angle 0.80231 / 0.35 (11015) hydrogen bonds : bond 0.04980 / 3.22 ( 293) hydrogen bonds : angle 3.76457 / 2.56 ( 758) metal coordination : bond 0.00570 / 0.28 ( 4) metal coordination : angle 4.18653 / 2.58 ( 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 66 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8220 (mt) cc_final: 0.7649 (mt) REVERT: A 388 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 483 GLN cc_start: 0.8212 (tt0) cc_final: 0.7938 (tt0) REVERT: A 630 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7055 (ptt180) REVERT: A 690 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7240 (mt-10) outliers start: 19 outliers final: 15 residues processed: 59 average time/residue: 0.1360 time to fit residues: 9.9651 Evaluate side-chains 62 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 569 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.202951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151296 restraints weight = 7966.609| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.45 r_work: 0.3727 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3814 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= 0.188 Angle : 0.834 9.630 11021 Z= 0.362 Chirality : 0.058 0.397 1265 Planarity : 0.005 0.059 1035 Dihedral : 17.499 177.959 1999 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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 are not related in a simple way. whole: -0.67 (0.34), residues: 615 helix: 0.68 (0.30), residues: 293 sheet: -1.80 (0.73), residues: 50 loop : -1.42 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 130 TYR 0.011 0.002 TYR A 175 PHE 0.017 0.002 PHE A 420 TRP 0.017 0.002 TRP A 82 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7770) covalent geometry : angle 0.82784 / 0.36 (11015) hydrogen bonds : bond 0.05066 / 3.28 ( 293) hydrogen bonds : angle 3.84709 / 2.61 ( 758) metal coordination : bond 0.00592 / 0.29 ( 4) metal coordination : angle 4.54185 / 2.80 ( 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: 17 poor density : 43 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8230 (mt) cc_final: 0.7657 (mt) REVERT: A 388 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 630 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7093 (ptt180) REVERT: A 690 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7114 (mt-10) outliers start: 17 outliers final: 14 residues processed: 53 average time/residue: 0.1363 time to fit residues: 8.9235 Evaluate side-chains 59 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 569 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4469 r_free = 0.4469 target = 0.207774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156131 restraints weight = 8048.610| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.50 r_work: 0.3767 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3816 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= 0.138 Angle : 0.804 9.949 11021 Z= 0.348 Chirality : 0.057 0.378 1265 Planarity : 0.005 0.061 1035 Dihedral : 17.486 176.726 1999 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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 are not related in a simple way. whole: -0.56 (0.34), residues: 615 helix: 0.82 (0.30), residues: 294 sheet: -1.86 (0.71), residues: 50 loop : -1.40 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 130 TYR 0.012 0.001 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 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7770) covalent geometry : angle 0.79920 / 0.35 (11015) hydrogen bonds : bond 0.04972 / 3.18 ( 293) hydrogen bonds : angle 3.73832 / 2.54 ( 758) metal coordination : bond 0.00527 / 0.25 ( 4) metal coordination : angle 4.02506 / 2.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.42 seconds wall clock time: 36 minutes 38.39 seconds (2198.39 seconds total)