Starting phenix.real_space_refine on Fri Dec 27 11:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz0_15030/12_2024/7zz0_15030.cif" } resolution = 2.26 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= 0.009 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 Mn 1 7.51 5 Mg 1 5.21 5 S 19 5.16 5 C 2736 2.51 5 N 731 2.21 5 O 899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4301 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Unusual residues: {' MG': 1, ' MN': 1} Classifications: {'undetermined': 2, 'water': 84} Link IDs: {None: 85} Time building chain proxies: 3.62, per 1000 atoms: 0.83 Number of scatterers: 4387 At special positions: 0 Unit cell: (71.02, 77.38, 79.5, 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) Mn 1 24.99 S 19 16.00 Mg 1 11.99 O 899 8.00 N 731 7.00 C 2736 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: 1.01 Conformation dependent library (CDL) restraints added in 541.3 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 62.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 551 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.796A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 644 through 658 removed outlier: 3.793A pdb=" N MET A 648 " --> pdb=" O TRP A 644 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.778A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 840 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 860 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 945 through 957 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.850A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 13.139A pdb=" N ARG A 606 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLY A 570 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1425 1.34 - 1.46: 976 1.46 - 1.58: 1958 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4396 Sorted by residual: bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CE KCX A 703 " pdb=" NZ KCX A 703 " ideal model delta sigma weight residual 1.442 1.487 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C LEU A 645 " pdb=" N PRO A 646 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.68e+00 bond pdb=" C ALA A 807 " pdb=" N PRO A 808 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.19e-02 7.06e+03 1.99e+00 bond pdb=" CG ASP A 723 " pdb=" OD1 ASP A 723 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.40e+00 ... (remaining 4391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 5807 1.93 - 3.85: 121 3.85 - 5.78: 14 5.78 - 7.70: 6 7.70 - 9.63: 3 Bond angle restraints: 5951 Sorted by residual: angle pdb=" CA MET A 822 " pdb=" CB MET A 822 " pdb=" CG MET A 822 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CB MET A 822 " pdb=" CG MET A 822 " pdb=" SD MET A 822 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta sigma weight residual 121.58 115.57 6.01 1.95e+00 2.63e-01 9.50e+00 angle pdb=" C VAL A 927 " pdb=" CA VAL A 927 " pdb=" CB VAL A 927 " ideal model delta sigma weight residual 110.98 114.52 -3.54 1.37e+00 5.33e-01 6.67e+00 angle pdb=" CA GLN A 749 " pdb=" CB GLN A 749 " pdb=" CG GLN A 749 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.56e+00 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2272 17.56 - 35.11: 269 35.11 - 52.67: 83 52.67 - 70.23: 18 70.23 - 87.78: 4 Dihedral angle restraints: 2646 sinusoidal: 1077 harmonic: 1569 Sorted by residual: dihedral pdb=" CA ARG A 533 " pdb=" C ARG A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE A 918 " pdb=" C PHE A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA MET A 705 " pdb=" CB MET A 705 " pdb=" CG MET A 705 " pdb=" SD MET A 705 " ideal model delta sinusoidal sigma weight residual -60.00 -119.93 59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 581 0.070 - 0.139: 62 0.139 - 0.209: 6 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 465 " pdb=" CB LEU A 465 " pdb=" CD1 LEU A 465 " pdb=" CD2 LEU A 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 552 " pdb=" CA ILE A 552 " pdb=" CG1 ILE A 552 " pdb=" CG2 ILE A 552 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 866 " pdb=" CA VAL A 866 " pdb=" CG1 VAL A 866 " pdb=" CG2 VAL A 866 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 647 not shown) Planarity restraints: 777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 614 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" CD GLN A 614 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 614 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 614 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 533 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ARG A 533 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 533 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP A 534 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 807 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 808 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.022 5.00e-02 4.00e+02 ... (remaining 774 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 172 2.70 - 3.25: 4348 3.25 - 3.80: 8091 3.80 - 4.35: 10268 4.35 - 4.90: 16365 Nonbonded interactions: 39244 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.149 2.320 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.157 2.320 nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.167 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1350 " model vdw 2.189 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.225 2.400 ... (remaining 39239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 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 : 0.004 0.083 4396 Z= 0.262 Angle : 0.707 9.630 5951 Z= 0.382 Chirality : 0.046 0.348 650 Planarity : 0.004 0.038 777 Dihedral : 16.824 87.784 1642 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.96 % Allowed : 15.47 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.34 (0.33), residues: 536 helix: -0.06 (0.27), residues: 293 sheet: -0.43 (0.71), residues: 45 loop : -0.14 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 799 HIS 0.004 0.001 HIS A 732 PHE 0.012 0.002 PHE A 879 TYR 0.012 0.001 TYR A 578 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.516 Fit side-chains REVERT: A 880 MET cc_start: 0.8393 (mtp) cc_final: 0.8105 (mtp) outliers start: 9 outliers final: 9 residues processed: 36 average time/residue: 1.2773 time to fit residues: 48.2712 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 882 GLN Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4396 Z= 0.179 Angle : 0.494 5.709 5951 Z= 0.262 Chirality : 0.041 0.189 650 Planarity : 0.004 0.034 777 Dihedral : 7.138 53.006 614 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.40 % Allowed : 14.16 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.97 (0.35), residues: 536 helix: 1.08 (0.29), residues: 297 sheet: -0.46 (0.71), residues: 45 loop : 0.45 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.009 0.001 PHE A 907 TYR 0.009 0.001 TYR A 775 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.525 Fit side-chains REVERT: A 928 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8480 (mttm) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 1.2416 time to fit residues: 45.6718 Evaluate side-chains 34 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4396 Z= 0.128 Angle : 0.452 5.007 5951 Z= 0.238 Chirality : 0.040 0.164 650 Planarity : 0.003 0.035 777 Dihedral : 6.384 53.506 605 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.18 % Allowed : 14.16 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.26 (0.36), residues: 536 helix: 1.41 (0.30), residues: 298 sheet: -0.44 (0.73), residues: 45 loop : 0.43 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.007 0.001 TYR A 830 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.544 Fit side-chains REVERT: A 460 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7037 (ttp-110) outliers start: 10 outliers final: 5 residues processed: 35 average time/residue: 1.2733 time to fit residues: 46.6722 Evaluate side-chains 32 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4396 Z= 0.208 Angle : 0.485 5.499 5951 Z= 0.256 Chirality : 0.041 0.203 650 Planarity : 0.003 0.036 777 Dihedral : 6.572 56.417 605 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 14.16 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.34 (0.35), residues: 536 helix: 1.51 (0.30), residues: 298 sheet: -0.52 (0.71), residues: 45 loop : 0.44 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.008 0.001 PHE A 636 TYR 0.010 0.001 TYR A 775 ARG 0.002 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.614 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 37 average time/residue: 1.4495 time to fit residues: 56.0268 Evaluate side-chains 33 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4396 Z= 0.203 Angle : 0.482 5.827 5951 Z= 0.255 Chirality : 0.041 0.213 650 Planarity : 0.003 0.036 777 Dihedral : 6.658 59.104 605 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.92 % Allowed : 13.29 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.36 (0.35), residues: 536 helix: 1.52 (0.30), residues: 298 sheet: -0.61 (0.70), residues: 45 loop : 0.50 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.009 0.001 PHE A 636 TYR 0.009 0.001 TYR A 775 ARG 0.002 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.549 Fit side-chains REVERT: A 893 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8458 (mtm110) outliers start: 18 outliers final: 10 residues processed: 40 average time/residue: 1.4380 time to fit residues: 60.2254 Evaluate side-chains 36 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 893 ARG Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 510 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4396 Z= 0.244 Angle : 0.511 6.102 5951 Z= 0.269 Chirality : 0.042 0.212 650 Planarity : 0.004 0.036 777 Dihedral : 6.689 58.244 605 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.49 % Allowed : 13.07 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.34 (0.35), residues: 536 helix: 1.51 (0.30), residues: 298 sheet: -0.74 (0.68), residues: 45 loop : 0.51 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.009 0.001 PHE A 636 TYR 0.009 0.001 TYR A 775 ARG 0.002 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.649 Fit side-chains REVERT: A 893 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8457 (mtm110) outliers start: 16 outliers final: 11 residues processed: 38 average time/residue: 1.2429 time to fit residues: 49.6629 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 893 ARG Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.3090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4396 Z= 0.133 Angle : 0.460 6.318 5951 Z= 0.239 Chirality : 0.040 0.225 650 Planarity : 0.003 0.035 777 Dihedral : 6.240 52.134 605 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.83 % Allowed : 14.38 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.47 (0.36), residues: 536 helix: 1.62 (0.30), residues: 298 sheet: -0.68 (0.71), residues: 45 loop : 0.56 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.009 0.001 PHE A 907 TYR 0.007 0.001 TYR A 830 ARG 0.001 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.561 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 37 average time/residue: 1.3929 time to fit residues: 53.8910 Evaluate side-chains 33 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4396 Z= 0.178 Angle : 0.487 7.435 5951 Z= 0.252 Chirality : 0.041 0.241 650 Planarity : 0.003 0.035 777 Dihedral : 6.275 51.735 605 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 14.60 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.48 (0.36), residues: 536 helix: 1.63 (0.30), residues: 298 sheet: -0.69 (0.71), residues: 45 loop : 0.56 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.540 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 35 average time/residue: 1.1702 time to fit residues: 43.0933 Evaluate side-chains 36 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4396 Z= 0.207 Angle : 0.504 7.781 5951 Z= 0.260 Chirality : 0.042 0.272 650 Planarity : 0.003 0.035 777 Dihedral : 6.325 51.413 605 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 14.60 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.44 (0.36), residues: 536 helix: 1.58 (0.30), residues: 298 sheet: -0.74 (0.70), residues: 45 loop : 0.56 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.009 0.001 PHE A 636 TYR 0.008 0.001 TYR A 685 ARG 0.002 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.541 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 34 average time/residue: 1.3398 time to fit residues: 47.7586 Evaluate side-chains 35 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4396 Z= 0.186 Angle : 0.498 8.362 5951 Z= 0.256 Chirality : 0.042 0.283 650 Planarity : 0.003 0.035 777 Dihedral : 6.227 51.490 605 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.18 % Allowed : 15.03 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.46 (0.36), residues: 536 helix: 1.60 (0.30), residues: 298 sheet: -0.72 (0.70), residues: 45 loop : 0.57 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.008 0.001 PHE A 636 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.534 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 34 average time/residue: 1.1527 time to fit residues: 41.2850 Evaluate side-chains 35 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045573 restraints weight = 14190.034| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.57 r_work: 0.2866 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4396 Z= 0.182 Angle : 0.496 8.147 5951 Z= 0.255 Chirality : 0.042 0.282 650 Planarity : 0.003 0.035 777 Dihedral : 6.179 51.523 605 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 15.03 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.45 (0.36), residues: 536 helix: 1.60 (0.30), residues: 298 sheet: -0.75 (0.70), residues: 45 loop : 0.58 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.15 seconds wall clock time: 32 minutes 9.52 seconds (1929.52 seconds total)