Starting phenix.real_space_refine on Fri Dec 27 22:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.map" model { file = "/net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sva_25446/12_2024/7sva_25446.cif" } resolution = 3.26 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 93 atoms to isotropic. 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 P 11 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4090 2.51 5 N 1159 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6290 Classifications: {'peptide': 792} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 747} Chain breaks: 5 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 1, 'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 6} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.81 Number of scatterers: 6515 At special positions: 0 Unit cell: (77.542, 95.088, 113.766, 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) S 37 16.00 P 11 15.00 Mg 1 11.99 O 1217 8.00 N 1159 7.00 C 4090 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: 1.87 Conformation dependent library (CDL) restraints added in 792.5 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 31.4% alpha, 17.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.690A pdb=" N LEU A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 removed outlier: 5.121A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.205A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.731A pdb=" N ALA A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.671A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 770 through 784 removed outlier: 3.703A pdb=" N ASP A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 821 removed outlier: 3.955A pdb=" N ILE A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.541A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing sheet with id=AA1, first strand: chain 'A' and resid 738 through 745 removed outlier: 3.751A pdb=" N ALA A 724 " --> pdb=" O CYS A 743 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE A 705 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 710 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 790 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 831 " --> pdb=" O ILE A 790 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A 792 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 833 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG A 794 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 318 removed outlier: 3.794A pdb=" N LEU A 322 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 503 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 7.179A pdb=" N GLN A 159 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 241 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 214 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 4.031A pdb=" N PHE A 311 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.600A pdb=" N VAL A 373 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 371 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394 removed outlier: 4.665A pdb=" N GLY A 389 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 432 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 391 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N CYS A 430 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.542A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597 removed outlier: 4.187A pdb=" N TYR A 596 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 556 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A 629 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 558 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS A 656 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 628 " --> pdb=" O CYS A 656 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2082 1.34 - 1.46: 1074 1.46 - 1.58: 3446 1.58 - 1.70: 21 1.70 - 1.81: 52 Bond restraints: 6675 Sorted by residual: bond pdb=" N SER A 720 " pdb=" CA SER A 720 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU A 718 " pdb=" CA GLU A 718 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.96e+00 bond pdb=" N ARG A 780 " pdb=" CA ARG A 780 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" N SER A 719 " pdb=" CA SER A 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.95e+00 bond pdb=" N ASN A 715 " pdb=" CA ASN A 715 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 ... (remaining 6670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 8950 2.22 - 4.43: 119 4.43 - 6.65: 10 6.65 - 8.86: 3 8.86 - 11.08: 2 Bond angle restraints: 9084 Sorted by residual: angle pdb=" N TRP A 732 " pdb=" CA TRP A 732 " pdb=" C TRP A 732 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" C LYS A 457 " pdb=" CA LYS A 457 " pdb=" CB LYS A 457 " ideal model delta sigma weight residual 116.34 110.51 5.83 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 127.38 -11.08 3.50e+00 8.16e-02 1.00e+01 angle pdb=" CA GLU A 718 " pdb=" C GLU A 718 " pdb=" O GLU A 718 " ideal model delta sigma weight residual 120.90 117.91 2.99 1.07e+00 8.73e-01 7.81e+00 angle pdb=" CA GLU A 717 " pdb=" C GLU A 717 " pdb=" O GLU A 717 " ideal model delta sigma weight residual 122.32 118.31 4.01 1.51e+00 4.39e-01 7.07e+00 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 3542 16.86 - 33.72: 407 33.72 - 50.58: 86 50.58 - 67.44: 36 67.44 - 84.30: 10 Dihedral angle restraints: 4081 sinusoidal: 1771 harmonic: 2310 Sorted by residual: dihedral pdb=" CA GLY A 856 " pdb=" C GLY A 856 " pdb=" N ASN A 857 " pdb=" CA ASN A 857 " ideal model delta harmonic sigma weight residual 180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP A 732 " pdb=" C TRP A 732 " pdb=" N PRO A 733 " pdb=" CA PRO A 733 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASN A 548 " pdb=" C ASN A 548 " pdb=" N GLY A 549 " pdb=" CA GLY A 549 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 859 0.056 - 0.112: 143 0.112 - 0.167: 14 0.167 - 0.223: 0 0.223 - 0.279: 1 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA TRP A 732 " pdb=" N TRP A 732 " pdb=" C TRP A 732 " pdb=" CB TRP A 732 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CB ILE A 701 " pdb=" CA ILE A 701 " pdb=" CG1 ILE A 701 " pdb=" CG2 ILE A 701 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1014 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.032 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" CG TRP A 732 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 695 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 696 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 732 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 733 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.031 5.00e-02 4.00e+02 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 76 2.64 - 3.21: 5713 3.21 - 3.77: 10012 3.77 - 4.34: 13415 4.34 - 4.90: 22923 Nonbonded interactions: 52139 Sorted by model distance: nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 709 " pdb="MG MG A1001 " model vdw 2.097 2.170 nonbonded pdb=" O ARG A 643 " pdb=" OG1 THR A 647 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 829 " pdb=" OD1 ASN A 900 " model vdw 2.177 3.040 nonbonded pdb=" OE1 GLU A 646 " pdb=" OH TYR A 944 " model vdw 2.192 3.040 ... (remaining 52134 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 0.060 6675 Z= 0.190 Angle : 0.595 11.079 9084 Z= 0.316 Chirality : 0.041 0.279 1017 Planarity : 0.005 0.089 1131 Dihedral : 15.797 84.303 2587 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.44 (0.32), residues: 780 helix: 1.87 (0.35), residues: 239 sheet: -1.04 (0.40), residues: 179 loop : -1.39 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP A 732 HIS 0.001 0.000 HIS A 427 PHE 0.011 0.001 PHE A 802 TYR 0.007 0.001 TYR A 312 ARG 0.006 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.3826 time to fit residues: 26.0844 Evaluate side-chains 26 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 0.0270 overall best weight: 2.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 489 ASN A 677 ASN A 715 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6675 Z= 0.236 Angle : 0.604 10.953 9084 Z= 0.304 Chirality : 0.042 0.156 1017 Planarity : 0.005 0.059 1131 Dihedral : 10.992 63.918 1033 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.43 % Allowed : 6.08 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.23 (0.32), residues: 780 helix: 2.03 (0.36), residues: 244 sheet: -0.83 (0.40), residues: 177 loop : -1.35 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 732 HIS 0.003 0.001 HIS A 427 PHE 0.013 0.001 PHE A 211 TYR 0.010 0.001 TYR A 596 ARG 0.005 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.3017 time to fit residues: 13.1700 Evaluate side-chains 28 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6675 Z= 0.200 Angle : 0.546 7.805 9084 Z= 0.278 Chirality : 0.041 0.151 1017 Planarity : 0.005 0.052 1131 Dihedral : 10.759 63.866 1033 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.58 % Allowed : 7.81 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.04 (0.32), residues: 780 helix: 2.15 (0.36), residues: 244 sheet: -0.65 (0.41), residues: 167 loop : -1.25 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 732 HIS 0.003 0.001 HIS A 427 PHE 0.011 0.001 PHE A 211 TYR 0.009 0.001 TYR A 596 ARG 0.004 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.7501 (mmm) cc_final: 0.6771 (tpt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.2804 time to fit residues: 13.0576 Evaluate side-chains 31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS A 823 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6675 Z= 0.300 Angle : 0.586 6.320 9084 Z= 0.300 Chirality : 0.042 0.148 1017 Planarity : 0.005 0.049 1131 Dihedral : 10.785 63.898 1032 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.30 % Allowed : 9.84 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.20 (0.31), residues: 780 helix: 2.05 (0.35), residues: 242 sheet: -0.83 (0.39), residues: 173 loop : -1.30 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 732 HIS 0.004 0.001 HIS A 427 PHE 0.010 0.001 PHE A 874 TYR 0.010 0.001 TYR A 596 ARG 0.006 0.001 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 38 average time/residue: 0.1953 time to fit residues: 10.5656 Evaluate side-chains 31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6675 Z= 0.188 Angle : 0.555 6.650 9084 Z= 0.281 Chirality : 0.041 0.149 1017 Planarity : 0.004 0.046 1131 Dihedral : 10.413 63.872 1029 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.72 % Allowed : 11.58 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.08 (0.32), residues: 780 helix: 2.16 (0.35), residues: 243 sheet: -0.74 (0.40), residues: 172 loop : -1.26 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 539 HIS 0.002 0.001 HIS A 894 PHE 0.009 0.001 PHE A 148 TYR 0.011 0.001 TYR A 893 ARG 0.004 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.7417 (mmm) cc_final: 0.6731 (tpt) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.2717 time to fit residues: 12.5708 Evaluate side-chains 31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 0.0770 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6675 Z= 0.340 Angle : 0.608 6.956 9084 Z= 0.309 Chirality : 0.042 0.145 1017 Planarity : 0.005 0.047 1131 Dihedral : 10.558 63.959 1029 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.87 % Allowed : 12.74 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.25 (0.31), residues: 780 helix: 2.00 (0.34), residues: 242 sheet: -0.85 (0.40), residues: 168 loop : -1.33 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 732 HIS 0.003 0.001 HIS A 894 PHE 0.009 0.002 PHE A 291 TYR 0.011 0.001 TYR A 596 ARG 0.006 0.001 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1980 time to fit residues: 9.4462 Evaluate side-chains 32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6675 Z= 0.152 Angle : 0.542 6.997 9084 Z= 0.272 Chirality : 0.040 0.146 1017 Planarity : 0.004 0.044 1131 Dihedral : 10.351 63.862 1029 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.58 % Allowed : 13.02 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.03 (0.31), residues: 780 helix: 2.28 (0.35), residues: 241 sheet: -0.67 (0.40), residues: 172 loop : -1.30 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 897 HIS 0.002 0.000 HIS A 838 PHE 0.009 0.001 PHE A 148 TYR 0.009 0.001 TYR A 893 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.7363 (mmm) cc_final: 0.6674 (tpt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.2359 time to fit residues: 11.4058 Evaluate side-chains 34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6675 Z= 0.262 Angle : 0.572 8.583 9084 Z= 0.287 Chirality : 0.041 0.198 1017 Planarity : 0.004 0.042 1131 Dihedral : 10.375 63.966 1029 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.43 % Allowed : 13.89 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.02 (0.31), residues: 780 helix: 2.25 (0.35), residues: 241 sheet: -0.64 (0.40), residues: 168 loop : -1.27 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 732 HIS 0.002 0.001 HIS A 894 PHE 0.008 0.001 PHE A 148 TYR 0.010 0.001 TYR A 596 ARG 0.004 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2410 time to fit residues: 11.3285 Evaluate side-chains 33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.0980 chunk 73 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 46 optimal weight: 8.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6675 Z= 0.137 Angle : 0.552 9.507 9084 Z= 0.275 Chirality : 0.040 0.187 1017 Planarity : 0.004 0.042 1131 Dihedral : 10.269 63.854 1029 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.14 % Allowed : 14.33 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.15 (0.31), residues: 780 helix: 2.38 (0.35), residues: 241 sheet: -0.41 (0.41), residues: 167 loop : -1.23 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 897 HIS 0.002 0.000 HIS A 838 PHE 0.009 0.001 PHE A 148 TYR 0.009 0.001 TYR A 893 ARG 0.008 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.7357 (mmm) cc_final: 0.6713 (tpp) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.2054 time to fit residues: 9.7954 Evaluate side-chains 29 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6675 Z= 0.375 Angle : 0.636 7.415 9084 Z= 0.319 Chirality : 0.043 0.179 1017 Planarity : 0.005 0.054 1131 Dihedral : 10.420 64.013 1029 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.43 % Allowed : 14.18 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.08 (0.31), residues: 780 helix: 2.15 (0.35), residues: 242 sheet: -0.48 (0.40), residues: 166 loop : -1.38 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 732 HIS 0.004 0.001 HIS A 894 PHE 0.010 0.002 PHE A 779 TYR 0.012 0.002 TYR A 596 ARG 0.005 0.001 ARG A 789 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.2219 time to fit residues: 10.1460 Evaluate side-chains 31 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.053525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039952 restraints weight = 34868.415| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.31 r_work: 0.2795 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6675 Z= 0.282 Angle : 0.592 7.726 9084 Z= 0.297 Chirality : 0.042 0.176 1017 Planarity : 0.005 0.045 1131 Dihedral : 10.404 63.952 1029 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.14 % Allowed : 14.76 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.12 (0.31), residues: 780 helix: 2.13 (0.34), residues: 241 sheet: -0.59 (0.40), residues: 170 loop : -1.36 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 732 HIS 0.002 0.001 HIS A 894 PHE 0.009 0.001 PHE A 148 TYR 0.010 0.001 TYR A 596 ARG 0.006 0.001 ARG A 562 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.50 seconds wall clock time: 31 minutes 49.03 seconds (1909.03 seconds total)