Starting phenix.real_space_refine on Thu Mar 6 02:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz0_15030/03_2025/7zz0_15030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz0_15030/03_2025/7zz0_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_15030/03_2025/7zz0_15030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz0_15030/03_2025/7zz0_15030.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz0_15030/03_2025/7zz0_15030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz0_15030/03_2025/7zz0_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-5624/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: 3.19, per 1000 atoms: 0.73 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: 1.06 Conformation dependent library (CDL) restraints added in 483.9 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: 0.47 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: 1.15 Time building geometry restraints manager: 1.26 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- 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 : 0.518 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: 1.2739 time to fit residues: 48.3370 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 : 0.547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.051038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046307 restraints weight = 13912.253| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.57 r_work: 0.2886 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4396 Z= 0.170 Angle : 0.491 5.742 5951 Z= 0.260 Chirality : 0.041 0.185 650 Planarity : 0.004 0.034 777 Dihedral : 7.149 53.060 614 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.21 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: 0.96 (0.35), residues: 536 helix: 1.08 (0.29), residues: 297 sheet: -0.47 (0.71), residues: 45 loop : 0.44 (0.44), residues: 194 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 0.008 0.001 TYR A 775 ARG 0.002 0.000 ARG A 460 *********************** 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 : 0.520 Fit side-chains REVERT: A 928 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8495 (mttm) outliers start: 11 outliers final: 5 residues processed: 35 average time/residue: 2.2941 time to fit residues: 83.8442 Evaluate side-chains 33 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.048895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044206 restraints weight = 14097.052| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.53 r_work: 0.2815 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4396 Z= 0.357 Angle : 0.559 5.600 5951 Z= 0.299 Chirality : 0.044 0.207 650 Planarity : 0.004 0.036 777 Dihedral : 6.021 51.661 599 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.61 % Allowed : 13.29 % Favored : 84.10 % 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: 1.16 (0.35), residues: 536 helix: 1.32 (0.29), residues: 297 sheet: -0.42 (0.69), residues: 45 loop : 0.39 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 569 HIS 0.007 0.001 HIS A 536 PHE 0.010 0.002 PHE A 809 TYR 0.014 0.002 TYR A 775 ARG 0.003 0.000 ARG A 854 *********************** 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 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.545 Fit side-chains REVERT: A 893 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mtm110) outliers start: 12 outliers final: 7 residues processed: 35 average time/residue: 1.9982 time to fit residues: 72.6890 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 : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU 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 893 ARG Chi-restraints excluded: chain A residue 934 THR 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 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045476 restraints weight = 14049.780| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.56 r_work: 0.2857 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4396 Z= 0.188 Angle : 0.480 5.227 5951 Z= 0.255 Chirality : 0.041 0.158 650 Planarity : 0.004 0.038 777 Dihedral : 5.768 52.129 599 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.61 % Allowed : 13.73 % 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: 1.32 (0.35), residues: 536 helix: 1.47 (0.30), residues: 298 sheet: -0.48 (0.69), residues: 45 loop : 0.47 (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 0.010 0.001 PHE A 879 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 606 *********************** 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 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.544 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 35 average time/residue: 1.1289 time to fit residues: 41.6021 Evaluate side-chains 32 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.049901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045148 restraints weight = 14407.103| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.60 r_work: 0.2845 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.214 Angle : 0.494 5.732 5951 Z= 0.261 Chirality : 0.041 0.194 650 Planarity : 0.004 0.037 777 Dihedral : 5.754 51.636 599 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.27 % Allowed : 12.85 % Favored : 83.88 % 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: 1.35 (0.35), residues: 536 helix: 1.52 (0.30), residues: 298 sheet: -0.60 (0.68), residues: 45 loop : 0.47 (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 0.008 0.001 TYR A 853 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 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.541 Fit side-chains REVERT: A 893 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8563 (mtm110) outliers start: 15 outliers final: 10 residues processed: 37 average time/residue: 1.3129 time to fit residues: 51.0593 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.049912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045225 restraints weight = 14124.240| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.57 r_work: 0.2850 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1263 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= 0.210 Angle : 0.486 6.057 5951 Z= 0.257 Chirality : 0.041 0.212 650 Planarity : 0.003 0.036 777 Dihedral : 5.724 51.440 599 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 : 3.27 % Allowed : 13.07 % 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: 1.36 (0.35), residues: 536 helix: 1.54 (0.30), residues: 298 sheet: -0.71 (0.67), residues: 45 loop : 0.48 (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 0.010 0.001 PHE A 879 TYR 0.007 0.001 TYR A 775 ARG 0.002 0.000 ARG A 606 *********************** 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: 15 poor density : 26 time to evaluate : 0.519 Fit side-chains REVERT: A 893 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8554 (mtm110) outliers start: 15 outliers final: 10 residues processed: 38 average time/residue: 1.1687 time to fit residues: 46.6547 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 : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.049876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045296 restraints weight = 14211.112| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.56 r_work: 0.2853 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.197 Angle : 0.489 6.385 5951 Z= 0.256 Chirality : 0.041 0.222 650 Planarity : 0.003 0.036 777 Dihedral : 5.693 51.519 599 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.70 % Allowed : 13.07 % Favored : 83.22 % 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: 1.40 (0.35), residues: 536 helix: 1.56 (0.30), residues: 298 sheet: -0.69 (0.68), residues: 45 loop : 0.51 (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 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 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 43 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.510 Fit side-chains REVERT: A 893 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (mtm110) outliers start: 17 outliers final: 11 residues processed: 39 average time/residue: 1.2024 time to fit residues: 49.0830 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 : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 858 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045582 restraints weight = 14122.611| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.56 r_work: 0.2864 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4396 Z= 0.173 Angle : 0.481 6.737 5951 Z= 0.250 Chirality : 0.041 0.249 650 Planarity : 0.003 0.037 777 Dihedral : 5.613 51.716 599 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 13.94 % 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: 1.43 (0.36), residues: 536 helix: 1.59 (0.30), residues: 298 sheet: -0.70 (0.69), residues: 45 loop : 0.53 (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 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 606 *********************** 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 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.496 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 36 average time/residue: 1.0886 time to fit residues: 41.3614 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 : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 926 ILE 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 18 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045360 restraints weight = 14306.378| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.57 r_work: 0.2858 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4396 Z= 0.190 Angle : 0.499 7.058 5951 Z= 0.257 Chirality : 0.042 0.280 650 Planarity : 0.003 0.037 777 Dihedral : 5.640 51.671 599 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.40 % Allowed : 14.81 % 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: 1.42 (0.36), residues: 536 helix: 1.58 (0.30), residues: 298 sheet: -0.73 (0.69), residues: 45 loop : 0.54 (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 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 606 *********************** 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 : 0.479 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 34 average time/residue: 1.0359 time to fit residues: 37.2628 Evaluate side-chains 34 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.050517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046011 restraints weight = 14090.362| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.56 r_work: 0.2882 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4396 Z= 0.151 Angle : 0.476 7.134 5951 Z= 0.246 Chirality : 0.041 0.285 650 Planarity : 0.003 0.037 777 Dihedral : 5.534 52.113 599 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.39 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: 1.48 (0.36), residues: 536 helix: 1.63 (0.30), residues: 298 sheet: -0.71 (0.70), residues: 45 loop : 0.58 (0.44), 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 0.009 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 606 ********************** 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 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.544 Fit side-chains REVERT: A 893 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8390 (mtm110) REVERT: A 928 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8446 (mttm) outliers start: 11 outliers final: 7 residues processed: 39 average time/residue: 1.3215 time to fit residues: 53.8490 Evaluate side-chains 35 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 867 THR Chi-restraints excluded: chain A residue 893 ARG Chi-restraints excluded: chain A residue 928 LYS 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 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.0050 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.050621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046068 restraints weight = 14182.875| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.57 r_work: 0.2884 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4396 Z= 0.154 Angle : 0.483 8.081 5951 Z= 0.248 Chirality : 0.041 0.278 650 Planarity : 0.003 0.037 777 Dihedral : 5.512 52.186 599 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.18 % Allowed : 15.25 % 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: 1.51 (0.36), residues: 536 helix: 1.65 (0.30), residues: 298 sheet: -0.71 (0.71), residues: 45 loop : 0.59 (0.44), 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 0.009 0.001 PHE A 907 TYR 0.008 0.001 TYR A 853 ARG 0.002 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.73 seconds wall clock time: 63 minutes 50.00 seconds (3830.00 seconds total)