Starting phenix.real_space_refine on Tue Feb 11 15:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnx_26022/02_2025/7tnx_26022.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 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 26 5.49 5 S 32 5.16 5 C 3581 2.51 5 N 976 2.21 5 O 1137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5753 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 265 Unusual residues: {'GTP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} 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 4302 SG CYS A 810 24.961 51.835 20.300 1.00 32.46 S ATOM 4741 SG CYS A 864 25.057 50.376 16.542 1.00 45.36 S ATOM 4780 SG CYS A 869 26.399 53.639 17.338 1.00 48.58 S Time building chain proxies: 4.15, per 1000 atoms: 0.72 Number of scatterers: 5753 At special positions: 0 Unit cell: (88.2, 92.4, 82.95, 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 32 16.00 P 26 15.00 O 1137 8.00 N 976 7.00 C 3581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 50.9% alpha, 12.2% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.840A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.789A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.625A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.652A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.863A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.625A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.845A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.830A pdb=" N GLN A 588 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.738A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.751A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 3.811A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.656A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 Processing helix chain 'A' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.500A pdb=" N ILE A 262 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.859A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.859A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.645A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.532A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA7, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.243A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1673 1.33 - 1.45: 895 1.45 - 1.57: 3253 1.57 - 1.69: 49 1.69 - 1.82: 45 Bond restraints: 5915 Sorted by residual: bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.19e+01 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.08e-02 8.57e+03 1.12e+01 bond pdb=" N VAL A 522 " pdb=" CA VAL A 522 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.09e-02 8.42e+03 1.01e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.460 1.485 -0.025 8.60e-03 1.35e+04 8.55e+00 bond pdb=" N VAL A 463 " pdb=" CA VAL A 463 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.11e-02 8.12e+03 8.10e+00 ... (remaining 5910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 6773 1.54 - 3.08: 1258 3.08 - 4.62: 51 4.62 - 6.16: 4 6.16 - 7.70: 2 Bond angle restraints: 8088 Sorted by residual: angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 113.71 108.96 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.88 5.68 1.27e+00 6.20e-01 2.00e+01 angle pdb=" N ARG A 728 " pdb=" CA ARG A 728 " pdb=" C ARG A 728 " ideal model delta sigma weight residual 114.04 108.87 5.17 1.24e+00 6.50e-01 1.74e+01 angle pdb=" N PHE A 789 " pdb=" CA PHE A 789 " pdb=" C PHE A 789 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N ILE A 790 " pdb=" CA ILE A 790 " pdb=" C ILE A 790 " ideal model delta sigma weight residual 110.62 106.64 3.98 1.14e+00 7.69e-01 1.22e+01 ... (remaining 8083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.34: 3337 19.34 - 38.68: 225 38.68 - 58.02: 43 58.02 - 77.36: 31 77.36 - 96.70: 10 Dihedral angle restraints: 3646 sinusoidal: 1740 harmonic: 1906 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 7.90 96.70 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " pdb=" OE1 GLU A 249 " ideal model delta sinusoidal sigma weight residual 0.00 88.06 -88.06 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 503 " pdb=" CG GLU A 503 " pdb=" CD GLU A 503 " pdb=" OE1 GLU A 503 " ideal model delta sinusoidal sigma weight residual 0.00 -84.83 84.83 1 3.00e+01 1.11e-03 9.71e+00 ... (remaining 3643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 418 0.039 - 0.079: 264 0.079 - 0.118: 180 0.118 - 0.158: 52 0.158 - 0.197: 5 Chirality restraints: 919 Sorted by residual: chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 916 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 347 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR A 347 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 347 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 303 " -0.013 2.00e-02 2.50e+03 1.15e-02 2.67e+00 pdb=" CG TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 303 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 303 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 303 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 303 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 746 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY A 746 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY A 746 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A 747 " 0.009 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 736 2.78 - 3.31: 5868 3.31 - 3.84: 9216 3.84 - 4.37: 11227 4.37 - 4.90: 18370 Nonbonded interactions: 45417 Sorted by model distance: nonbonded pdb=" O2 U B 12 " pdb=" N2 G C 14 " model vdw 2.247 3.120 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.288 3.040 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASN A 259 " pdb=" N VAL A 405 " model vdw 2.322 3.120 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.394 3.120 ... (remaining 45412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.740 Find NCS groups from input model: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.011 0.045 5915 Z= 0.680 Angle : 1.082 7.703 8088 Z= 0.785 Chirality : 0.065 0.197 919 Planarity : 0.004 0.025 943 Dihedral : 15.461 96.698 2404 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.67 % Favored : 92.18 % Rotamer: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.31), residues: 639 helix: -0.49 (0.29), residues: 294 sheet: -2.90 (0.51), residues: 72 loop : -3.04 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 873 HIS 0.012 0.002 HIS A 876 PHE 0.018 0.003 PHE A 853 TYR 0.021 0.004 TYR A 303 ARG 0.005 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.651 Fit side-chains REVERT: A 340 ASN cc_start: 0.8342 (m-40) cc_final: 0.8062 (m110) REVERT: A 369 MET cc_start: 0.7396 (mtt) cc_final: 0.7022 (mtp) REVERT: A 607 GLU cc_start: 0.8801 (tp30) cc_final: 0.7765 (mt-10) REVERT: A 635 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7716 (ttmm) REVERT: A 715 TYR cc_start: 0.8385 (t80) cc_final: 0.7978 (t80) REVERT: A 716 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 867 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7594 (mm-40) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2322 time to fit residues: 37.3392 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103869 restraints weight = 6811.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107472 restraints weight = 4349.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109900 restraints weight = 3262.317| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5915 Z= 0.195 Angle : 0.530 8.686 8088 Z= 0.261 Chirality : 0.039 0.223 919 Planarity : 0.004 0.039 943 Dihedral : 14.239 90.769 1063 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 1.71 % Allowed : 10.62 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.33), residues: 639 helix: 0.96 (0.30), residues: 295 sheet: -2.55 (0.55), residues: 72 loop : -2.45 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 873 HIS 0.003 0.001 HIS A 871 PHE 0.010 0.001 PHE A 856 TYR 0.007 0.001 TYR A 246 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.606 Fit side-chains REVERT: A 255 MET cc_start: 0.8561 (mtt) cc_final: 0.8326 (mtm) REVERT: A 369 MET cc_start: 0.7718 (mtt) cc_final: 0.7463 (mtp) REVERT: A 607 GLU cc_start: 0.8397 (tp30) cc_final: 0.7758 (mt-10) REVERT: A 635 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7513 (ttmm) REVERT: A 715 TYR cc_start: 0.8646 (t80) cc_final: 0.8369 (t80) REVERT: A 867 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7600 (mm-40) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.1961 time to fit residues: 26.1106 Evaluate side-chains 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 444 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104667 restraints weight = 6815.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108277 restraints weight = 4345.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110719 restraints weight = 3258.539| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5915 Z= 0.154 Angle : 0.510 10.304 8088 Z= 0.247 Chirality : 0.038 0.163 919 Planarity : 0.004 0.039 943 Dihedral : 14.182 90.412 1062 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 2.57 % Allowed : 12.50 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.35), residues: 639 helix: 1.65 (0.31), residues: 294 sheet: -2.14 (0.59), residues: 72 loop : -2.14 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 PHE 0.011 0.001 PHE A 459 TYR 0.011 0.001 TYR A 622 ARG 0.008 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.660 Fit side-chains REVERT: A 346 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8410 (pp) REVERT: A 369 MET cc_start: 0.7714 (mtt) cc_final: 0.7483 (mtp) REVERT: A 422 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 607 GLU cc_start: 0.8450 (tp30) cc_final: 0.7816 (mt-10) REVERT: A 635 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7517 (ttmm) REVERT: A 641 ASP cc_start: 0.8137 (t0) cc_final: 0.7881 (t0) REVERT: A 715 TYR cc_start: 0.8670 (t80) cc_final: 0.8402 (t80) REVERT: A 867 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7623 (mm-40) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.1568 time to fit residues: 21.1706 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105235 restraints weight = 6921.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109236 restraints weight = 4261.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111984 restraints weight = 3119.609| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5915 Z= 0.144 Angle : 0.514 11.097 8088 Z= 0.249 Chirality : 0.038 0.224 919 Planarity : 0.003 0.039 943 Dihedral : 14.090 89.324 1062 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 3.42 % Allowed : 13.53 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.35), residues: 639 helix: 1.85 (0.31), residues: 295 sheet: -2.16 (0.57), residues: 80 loop : -2.04 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.003 0.000 HIS A 375 PHE 0.009 0.001 PHE A 459 TYR 0.007 0.001 TYR A 622 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.670 Fit side-chains REVERT: A 369 MET cc_start: 0.7720 (mtt) cc_final: 0.7478 (mtp) REVERT: A 393 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 434 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8011 (tp) REVERT: A 635 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7476 (ttmm) REVERT: A 715 TYR cc_start: 0.8631 (t80) cc_final: 0.8342 (t80) REVERT: A 867 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7634 (mm-40) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.1808 time to fit residues: 24.5497 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 384 ASN A 608 ASN A 769 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098694 restraints weight = 6869.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102450 restraints weight = 4299.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105026 restraints weight = 3178.425| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5915 Z= 0.257 Angle : 0.574 11.071 8088 Z= 0.277 Chirality : 0.040 0.207 919 Planarity : 0.004 0.043 943 Dihedral : 14.011 91.816 1062 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 3.42 % Allowed : 15.07 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.35), residues: 639 helix: 1.72 (0.31), residues: 296 sheet: -1.89 (0.62), residues: 74 loop : -2.07 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 873 HIS 0.005 0.001 HIS A 871 PHE 0.011 0.001 PHE A 856 TYR 0.013 0.001 TYR A 622 ARG 0.008 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.592 Fit side-chains REVERT: A 369 MET cc_start: 0.7756 (mtt) cc_final: 0.7489 (mtp) REVERT: A 422 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 434 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 607 GLU cc_start: 0.8527 (tp30) cc_final: 0.7823 (mt-10) REVERT: A 635 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7678 (ttmm) REVERT: A 867 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7664 (mm-40) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.1656 time to fit residues: 19.5395 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102446 restraints weight = 6833.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106058 restraints weight = 4429.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108466 restraints weight = 3324.745| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5915 Z= 0.185 Angle : 0.538 10.580 8088 Z= 0.260 Chirality : 0.039 0.181 919 Planarity : 0.004 0.041 943 Dihedral : 13.999 90.392 1062 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 3.42 % Allowed : 14.90 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.35), residues: 639 helix: 1.80 (0.31), residues: 296 sheet: -1.79 (0.63), residues: 74 loop : -1.95 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 PHE 0.010 0.001 PHE A 856 TYR 0.010 0.001 TYR A 313 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.610 Fit side-chains REVERT: A 255 MET cc_start: 0.8502 (mpp) cc_final: 0.8269 (mtm) REVERT: A 369 MET cc_start: 0.7734 (mtt) cc_final: 0.7504 (mtp) REVERT: A 422 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7160 (mt-10) REVERT: A 434 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 445 ASN cc_start: 0.8598 (m110) cc_final: 0.8366 (m110) REVERT: A 591 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 607 GLU cc_start: 0.8491 (tp30) cc_final: 0.7814 (mt-10) REVERT: A 635 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7571 (ttmm) outliers start: 20 outliers final: 18 residues processed: 97 average time/residue: 0.1514 time to fit residues: 20.3206 Evaluate side-chains 96 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6343 > 50: distance: 25 - 30: 29.549 distance: 30 - 31: 9.389 distance: 31 - 34: 27.490 distance: 32 - 33: 40.716 distance: 32 - 35: 27.233 distance: 35 - 36: 14.748 distance: 36 - 39: 5.585 distance: 37 - 38: 13.484 distance: 39 - 40: 6.793 distance: 41 - 42: 37.537 distance: 42 - 43: 30.352 distance: 42 - 45: 16.715 distance: 43 - 44: 56.459 distance: 45 - 46: 9.907 distance: 45 - 47: 34.686 distance: 48 - 49: 37.659 distance: 49 - 50: 69.369 distance: 50 - 52: 42.063 distance: 52 - 53: 24.946 distance: 53 - 54: 45.914 distance: 53 - 56: 10.078 distance: 54 - 55: 34.164 distance: 54 - 59: 24.192 distance: 56 - 58: 55.048 distance: 59 - 60: 22.228 distance: 60 - 61: 57.624 distance: 61 - 63: 56.911 distance: 63 - 64: 8.980 distance: 64 - 65: 21.742 distance: 64 - 67: 31.268 distance: 65 - 66: 24.915 distance: 65 - 71: 45.026 distance: 67 - 68: 32.965 distance: 68 - 69: 55.749 distance: 68 - 70: 57.189 distance: 71 - 72: 13.770 distance: 72 - 73: 56.835 distance: 72 - 75: 48.302 distance: 73 - 74: 39.558 distance: 73 - 76: 56.097 distance: 76 - 77: 47.226 distance: 77 - 78: 21.676 distance: 77 - 80: 48.884 distance: 78 - 79: 14.055 distance: 78 - 85: 43.172 distance: 80 - 81: 3.671 distance: 82 - 83: 14.562 distance: 83 - 84: 70.634 distance: 85 - 86: 16.989 distance: 86 - 87: 23.935 distance: 87 - 88: 27.512 distance: 87 - 93: 20.852 distance: 88 - 116: 31.674 distance: 89 - 90: 44.504 distance: 90 - 91: 18.511 distance: 90 - 92: 22.264