Starting phenix.real_space_refine on Thu Jul 2 00:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz0_15030/07_2026/7zz0_15030.map" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 0.95, per 1000 atoms: 0.22 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: 0.36 Conformation dependent library (CDL) restraints added in 261.1 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: 0.13 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: 0.69 Time building geometry restraints manager: 0.50 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: 2.570 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 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= 0.185 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (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 ARG 0.004 0.000 ARG A 606 TYR 0.012 0.001 TYR A 578 PHE 0.012 0.002 PHE A 879 TRP 0.004 0.001 TRP A 799 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 4396) covalent geometry : angle 0.70688 / 0.38 ( 5951) hydrogen bonds : bond 0.15653 / 9.67 ( 222) hydrogen bonds : angle 7.39772 / 5.36 ( 639) *********************** 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 : 0.113 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: 0.5005 time to fit residues: 18.7834 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 : 0.134 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3116 r_free = 0.3116 target = 0.050161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045362 restraints weight = 14193.459| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.59 r_work: 0.2852 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 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 : 0.004 0.022 4396 Z= 0.167 Angle : 0.520 6.008 5951 Z= 0.277 Chirality : 0.042 0.198 650 Planarity : 0.004 0.035 777 Dihedral : 7.281 52.455 614 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.18 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.35), residues: 536 helix: 1.09 (0.29), residues: 296 sheet: -0.42 (0.71), residues: 45 loop : 0.42 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 606 TYR 0.011 0.001 TYR A 775 PHE 0.009 0.001 PHE A 907 TRP 0.006 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 4396) covalent geometry : angle 0.51973 / 0.28 ( 5951) hydrogen bonds : bond 0.04864 / 3.23 ( 222) hydrogen bonds : angle 5.62948 / 4.11 ( 639) *********************** 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 36 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.138 Fit side-chains REVERT: A 460 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7011 (ttp-110) outliers start: 10 outliers final: 6 residues processed: 33 average time/residue: 0.5229 time to fit residues: 18.0405 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 : 0.165 ------------------------------------------------------------------------------- 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 967 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3096 r_free = 0.3096 target = 0.049534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044768 restraints weight = 14088.031| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.55 r_work: 0.2830 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4396 Z= 0.189 Angle : 0.520 5.358 5951 Z= 0.278 Chirality : 0.042 0.195 650 Planarity : 0.004 0.037 777 Dihedral : 6.824 59.820 605 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.27 % Allowed : 12.42 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.35), residues: 536 helix: 1.34 (0.29), residues: 297 sheet: -0.44 (0.69), residues: 45 loop : 0.38 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.012 0.001 TYR A 775 PHE 0.010 0.002 PHE A 879 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 4396) covalent geometry : angle 0.52031 / 0.28 ( 5951) hydrogen bonds : bond 0.04984 / 3.34 ( 222) hydrogen bonds : angle 5.46989 / 3.99 ( 639) *********************** 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 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.164 Fit side-chains REVERT: A 893 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8517 (mtm110) outliers start: 15 outliers final: 9 residues processed: 37 average time/residue: 0.4593 time to fit residues: 17.6834 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 : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG 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 867 THR 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 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3103 r_free = 0.3103 target = 0.049740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045019 restraints weight = 13906.026| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.56 r_work: 0.2841 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4396 Z= 0.164 Angle : 0.499 5.343 5951 Z= 0.266 Chirality : 0.042 0.167 650 Planarity : 0.004 0.038 777 Dihedral : 6.753 59.928 605 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.27 % Allowed : 12.42 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.35), residues: 536 helix: 1.48 (0.30), residues: 297 sheet: -0.53 (0.68), residues: 45 loop : 0.42 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.009 0.001 TYR A 775 PHE 0.009 0.001 PHE A 879 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4396) covalent geometry : angle 0.49942 / 0.27 ( 5951) hydrogen bonds : bond 0.04647 / 3.12 ( 222) hydrogen bonds : angle 5.33415 / 3.88 ( 639) *********************** 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 43 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.163 Fit side-chains REVERT: A 893 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8513 (mtm110) outliers start: 15 outliers final: 10 residues processed: 39 average time/residue: 0.4193 time to fit residues: 17.1088 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 676 SER 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 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 30 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3088 r_free = 0.3088 target = 0.049241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044559 restraints weight = 14075.664| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.54 r_work: 0.2825 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4396 Z= 0.200 Angle : 0.525 5.738 5951 Z= 0.280 Chirality : 0.043 0.209 650 Planarity : 0.004 0.037 777 Dihedral : 6.759 58.721 605 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.70 % Allowed : 12.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.35), residues: 536 helix: 1.50 (0.30), residues: 297 sheet: -0.65 (0.67), residues: 45 loop : 0.40 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 854 TYR 0.010 0.002 TYR A 775 PHE 0.011 0.002 PHE A 879 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 4396) covalent geometry : angle 0.52468 / 0.28 ( 5951) hydrogen bonds : bond 0.04986 / 3.36 ( 222) hydrogen bonds : angle 5.39319 / 3.91 ( 639) *********************** 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 43 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.103 Fit side-chains REVERT: A 893 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (mtm110) outliers start: 17 outliers final: 11 residues processed: 39 average time/residue: 0.4019 time to fit residues: 16.3622 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 : 0.105 ------------------------------------------------------------------------------- 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 676 SER 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 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 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN ** 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 = 0.3123 r_free = 0.3123 target = 0.050325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045575 restraints weight = 14371.911| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.59 r_work: 0.2862 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.1266 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= 0.124 Angle : 0.475 5.977 5951 Z= 0.251 Chirality : 0.041 0.218 650 Planarity : 0.003 0.037 777 Dihedral : 6.413 51.545 605 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.49 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.36), residues: 536 helix: 1.56 (0.30), residues: 298 sheet: -0.66 (0.68), residues: 45 loop : 0.44 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.008 0.001 TYR A 853 PHE 0.010 0.001 PHE A 907 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4396) covalent geometry : angle 0.47537 / 0.25 ( 5951) hydrogen bonds : bond 0.04151 / 2.78 ( 222) hydrogen bonds : angle 5.17216 / 3.75 ( 639) *********************** 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 42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.110 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 39 average time/residue: 0.4158 time to fit residues: 16.9013 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 : 0.142 ------------------------------------------------------------------------------- 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 814 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3115 r_free = 0.3115 target = 0.050041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045308 restraints weight = 14270.094| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.58 r_work: 0.2852 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 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 0.022 4396 Z= 0.141 Angle : 0.490 6.446 5951 Z= 0.257 Chirality : 0.042 0.226 650 Planarity : 0.003 0.037 777 Dihedral : 6.383 51.445 605 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.36), residues: 536 helix: 1.56 (0.30), residues: 298 sheet: -0.70 (0.68), residues: 45 loop : 0.50 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.007 0.001 TYR A 830 PHE 0.009 0.001 PHE A 879 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4396) covalent geometry : angle 0.48973 / 0.26 ( 5951) hydrogen bonds : bond 0.04330 / 2.91 ( 222) hydrogen bonds : angle 5.17583 / 3.75 ( 639) *********************** 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 42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.194 Fit side-chains REVERT: A 893 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8527 (mtm110) outliers start: 16 outliers final: 12 residues processed: 39 average time/residue: 0.4921 time to fit residues: 20.0572 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 814 THR 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 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 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3095 r_free = 0.3095 target = 0.049365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044818 restraints weight = 14335.631| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.56 r_work: 0.2839 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1302 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= 0.164 Angle : 0.517 6.806 5951 Z= 0.269 Chirality : 0.042 0.257 650 Planarity : 0.004 0.037 777 Dihedral : 6.445 51.158 605 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.49 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.35), residues: 536 helix: 1.55 (0.30), residues: 297 sheet: -0.73 (0.67), residues: 45 loop : 0.49 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 854 TYR 0.008 0.001 TYR A 775 PHE 0.010 0.001 PHE A 879 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4396) covalent geometry : angle 0.51727 / 0.27 ( 5951) hydrogen bonds : bond 0.04566 / 3.07 ( 222) hydrogen bonds : angle 5.24020 / 3.79 ( 639) *********************** 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 42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.179 Fit side-chains REVERT: A 893 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8421 (mtm110) outliers start: 16 outliers final: 12 residues processed: 39 average time/residue: 0.4308 time to fit residues: 17.5621 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 814 THR 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 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 42 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3106 r_free = 0.3106 target = 0.049716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045174 restraints weight = 14348.255| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.57 r_work: 0.2852 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.1299 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= 0.141 Angle : 0.499 6.995 5951 Z= 0.259 Chirality : 0.042 0.282 650 Planarity : 0.003 0.037 777 Dihedral : 6.325 51.364 605 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.27 % Allowed : 13.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.36), residues: 536 helix: 1.53 (0.30), residues: 298 sheet: -0.76 (0.68), residues: 45 loop : 0.50 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.007 0.001 TYR A 830 PHE 0.009 0.001 PHE A 907 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4396) covalent geometry : angle 0.49868 / 0.26 ( 5951) hydrogen bonds : bond 0.04312 / 2.89 ( 222) hydrogen bonds : angle 5.18349 / 3.75 ( 639) *********************** 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 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.136 Fit side-chains REVERT: A 893 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8490 (mtm110) outliers start: 15 outliers final: 12 residues processed: 39 average time/residue: 0.4336 time to fit residues: 17.6837 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 676 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 814 THR 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 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 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3135 r_free = 0.3135 target = 0.050577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046048 restraints weight = 14128.184| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.56 r_work: 0.2884 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.1332 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= 0.105 Angle : 0.475 7.134 5951 Z= 0.245 Chirality : 0.041 0.280 650 Planarity : 0.003 0.038 777 Dihedral : 5.979 52.158 605 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.36), residues: 536 helix: 1.60 (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 ARG 0.002 0.000 ARG A 606 TYR 0.008 0.001 TYR A 853 PHE 0.009 0.001 PHE A 907 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 4396) covalent geometry : angle 0.47539 / 0.25 ( 5951) hydrogen bonds : bond 0.03792 / 2.53 ( 222) hydrogen bonds : angle 5.03612 / 3.65 ( 639) ********************** 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 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.121 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 37 average time/residue: 0.4593 time to fit residues: 17.8662 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 : 0.162 ------------------------------------------------------------------------------- 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 676 SER Chi-restraints excluded: chain A residue 813 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 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3089 r_free = 0.3089 target = 0.049239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044515 restraints weight = 14258.179| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.55 r_work: 0.2824 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4396 Z= 0.214 Angle : 0.568 8.679 5951 Z= 0.292 Chirality : 0.044 0.306 650 Planarity : 0.004 0.035 777 Dihedral : 6.499 51.819 605 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.83 % Allowed : 14.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.35), residues: 536 helix: 1.54 (0.30), residues: 297 sheet: -0.81 (0.66), residues: 45 loop : 0.49 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.011 0.002 TYR A 776 PHE 0.010 0.002 PHE A 636 TRP 0.007 0.002 TRP A 569 HIS 0.006 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 4396) covalent geometry : angle 0.56835 / 0.29 ( 5951) hydrogen bonds : bond 0.05003 / 3.38 ( 222) hydrogen bonds : angle 5.31082 / 3.84 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1288.31 seconds wall clock time: 22 minutes 43.97 seconds (1363.97 seconds total)