Starting phenix.real_space_refine on Fri Dec 27 11:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz2_15032/12_2024/7zz2_15032.cif" } resolution = 2.48 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 2739 2.51 5 N 731 2.21 5 O 875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4366 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 65 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3, 'water': 57} Link IDs: {None: 59} Time building chain proxies: 3.28, per 1000 atoms: 0.75 Number of scatterers: 4366 At special positions: 0 Unit cell: (67.84, 76.32, 78.44, 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 875 8.00 N 731 7.00 C 2739 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: 1.37 Conformation dependent library (CDL) restraints added in 522.9 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 62.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 511 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 550 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.818A 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 645 through 658 removed outlier: 4.318A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.515A pdb=" N TYR A 685 " --> pdb=" O ASN A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 734 through 738 removed outlier: 4.622A pdb=" N SER A 737 " --> pdb=" O HIS A 734 " (cutoff:3.500A) 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: 3.790A 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 883 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 945 through 958 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: 6.885A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 633 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: 1.36 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1418 1.34 - 1.46: 878 1.46 - 1.58: 2068 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4401 Sorted by residual: bond pdb=" C1 PYR A1203 " pdb=" C2 PYR A1203 " ideal model delta sigma weight residual 1.558 1.388 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C2 PYR A1203 " pdb=" O3 PYR A1203 " ideal model delta sigma weight residual 1.210 1.309 -0.099 2.00e-02 2.50e+03 2.44e+01 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 1.74e+01 bond pdb=" C1 PYR A1203 " pdb=" O1 PYR A1203 " ideal model delta sigma weight residual 1.239 1.307 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 PYR A1203 " pdb=" O2 PYR A1203 " ideal model delta sigma weight residual 1.243 1.308 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 5844 2.28 - 4.55: 88 4.55 - 6.83: 19 6.83 - 9.10: 3 9.10 - 11.38: 3 Bond angle restraints: 5957 Sorted by residual: angle pdb=" CB MET A 982 " pdb=" CG MET A 982 " pdb=" SD MET A 982 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLN A 817 " pdb=" CB GLN A 817 " pdb=" CG GLN A 817 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CB MET A 858 " pdb=" CG MET A 858 " pdb=" SD MET A 858 " ideal model delta sigma weight residual 112.70 123.53 -10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA LYS A 921 " pdb=" CB LYS A 921 " pdb=" CG LYS A 921 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CB GLU A 960 " pdb=" CG GLU A 960 " pdb=" CD GLU A 960 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 5952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2293 17.82 - 35.65: 263 35.65 - 53.47: 62 53.47 - 71.30: 23 71.30 - 89.12: 6 Dihedral angle restraints: 2647 sinusoidal: 1078 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 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+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 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU A 583 " pdb=" CG GLU A 583 " pdb=" CD GLU A 583 " pdb=" OE1 GLU A 583 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 480 0.047 - 0.094: 137 0.094 - 0.141: 28 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+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 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB VAL A 840 " pdb=" CA VAL A 840 " pdb=" CG1 VAL A 840 " pdb=" CG2 VAL A 840 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 647 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 899 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 900 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 749 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CD GLN A 749 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN A 749 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 749 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 768 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 769 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " -0.020 5.00e-02 4.00e+02 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 140 2.69 - 3.24: 4250 3.24 - 3.79: 7930 3.79 - 4.35: 10233 4.35 - 4.90: 16234 Nonbonded interactions: 38787 Sorted by model distance: nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.132 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1308 " model vdw 2.176 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.202 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.213 2.320 nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.216 2.320 ... (remaining 38782 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: 1.570 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.050 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 : 0.005 0.170 4401 Z= 0.313 Angle : 0.764 11.381 5957 Z= 0.407 Chirality : 0.046 0.235 650 Planarity : 0.005 0.040 779 Dihedral : 17.253 89.122 1643 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.27 % Allowed : 18.95 % Favored : 77.78 % 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: -0.30 (0.33), residues: 536 helix: -0.15 (0.27), residues: 299 sheet: -0.07 (0.79), residues: 43 loop : 0.01 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 586 HIS 0.009 0.001 HIS A 823 PHE 0.011 0.002 PHE A 997 TYR 0.010 0.002 TYR A 578 ARG 0.006 0.001 ARG A 485 *********************** 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 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.518 Fit side-chains REVERT: A 596 MET cc_start: 0.9184 (mtp) cc_final: 0.8926 (mtm) outliers start: 15 outliers final: 14 residues processed: 45 average time/residue: 0.9491 time to fit residues: 45.4131 Evaluate side-chains 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 934 THR 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: 0.9980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 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 749 GLN A 999 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.189 Angle : 0.489 5.247 5957 Z= 0.261 Chirality : 0.040 0.137 650 Planarity : 0.004 0.035 779 Dihedral : 7.149 58.849 615 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.92 % Allowed : 16.12 % Favored : 79.96 % 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: 0.94 (0.35), residues: 536 helix: 1.02 (0.29), residues: 300 sheet: -0.08 (0.77), residues: 43 loop : 0.38 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.008 0.001 PHE A 907 TYR 0.008 0.001 TYR A 776 ARG 0.002 0.000 ARG A 593 *********************** 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 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.550 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 43 average time/residue: 1.0355 time to fit residues: 47.0505 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 : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.213 Angle : 0.494 6.029 5957 Z= 0.261 Chirality : 0.041 0.132 650 Planarity : 0.004 0.033 779 Dihedral : 6.238 55.887 603 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.70 % Allowed : 18.08 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.36), residues: 536 helix: 1.52 (0.30), residues: 294 sheet: -0.15 (0.75), residues: 43 loop : 0.59 (0.45), residues: 199 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 680 ARG 0.002 0.000 ARG A 588 *********************** 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 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.528 Fit side-chains REVERT: A 596 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8956 (mtm) outliers start: 17 outliers final: 10 residues processed: 40 average time/residue: 1.2748 time to fit residues: 53.3914 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 : 0.515 ------------------------------------------------------------------------------- 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 596 MET Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0470 chunk 36 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4401 Z= 0.157 Angle : 0.460 4.981 5957 Z= 0.242 Chirality : 0.040 0.133 650 Planarity : 0.003 0.031 779 Dihedral : 6.043 52.116 602 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.92 % Allowed : 17.86 % Favored : 78.21 % 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: 1.58 (0.36), residues: 536 helix: 1.69 (0.30), residues: 295 sheet: -0.26 (0.75), residues: 43 loop : 0.56 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.008 0.001 PHE A 636 TYR 0.006 0.001 TYR A 680 ARG 0.001 0.000 ARG A 588 *********************** 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 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.566 Fit side-chains REVERT: A 596 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8956 (mtm) outliers start: 18 outliers final: 9 residues processed: 40 average time/residue: 1.1741 time to fit residues: 49.4611 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 596 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4401 Z= 0.235 Angle : 0.497 6.863 5957 Z= 0.262 Chirality : 0.041 0.133 650 Planarity : 0.003 0.030 779 Dihedral : 6.092 49.934 602 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.05 % Allowed : 18.74 % Favored : 78.21 % 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: 1.64 (0.36), residues: 536 helix: 1.76 (0.30), residues: 295 sheet: -0.26 (0.74), residues: 43 loop : 0.54 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 PHE 0.008 0.001 PHE A 636 TYR 0.009 0.001 TYR A 776 ARG 0.003 0.000 ARG A 845 *********************** 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: 14 poor density : 29 time to evaluate : 0.484 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 38 average time/residue: 1.0646 time to fit residues: 42.7593 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 : 0.586 ------------------------------------------------------------------------------- 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 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4401 Z= 0.243 Angle : 0.499 5.422 5957 Z= 0.264 Chirality : 0.042 0.136 650 Planarity : 0.003 0.030 779 Dihedral : 6.141 50.879 602 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.05 % Allowed : 18.74 % Favored : 78.21 % 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: 1.64 (0.36), residues: 536 helix: 1.74 (0.30), residues: 295 sheet: -0.28 (0.74), residues: 43 loop : 0.57 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.009 0.001 PHE A 907 TYR 0.009 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 *********************** 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: 14 poor density : 28 time to evaluate : 0.531 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 37 average time/residue: 1.0881 time to fit residues: 42.5277 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.203 Angle : 0.494 7.675 5957 Z= 0.258 Chirality : 0.041 0.136 650 Planarity : 0.003 0.030 779 Dihedral : 6.108 52.039 602 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.61 % Allowed : 19.17 % Favored : 78.21 % 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: 1.66 (0.36), residues: 536 helix: 1.76 (0.30), residues: 295 sheet: -0.31 (0.74), residues: 43 loop : 0.57 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.008 0.001 PHE A 879 TYR 0.008 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.510 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 36 average time/residue: 1.0344 time to fit residues: 39.3786 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 465 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4401 Z= 0.168 Angle : 0.483 7.465 5957 Z= 0.250 Chirality : 0.040 0.136 650 Planarity : 0.003 0.030 779 Dihedral : 6.043 53.115 602 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.18 % Allowed : 19.39 % Favored : 78.43 % 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: 1.55 (0.36), residues: 536 helix: 1.67 (0.30), residues: 301 sheet: -0.33 (0.73), residues: 43 loop : 0.50 (0.45), residues: 192 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 879 TYR 0.007 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 *********************** 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 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.569 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 35 average time/residue: 1.0823 time to fit residues: 40.0540 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 : 0.518 ------------------------------------------------------------------------------- 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 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4401 Z= 0.222 Angle : 0.527 11.025 5957 Z= 0.269 Chirality : 0.041 0.143 650 Planarity : 0.003 0.030 779 Dihedral : 6.107 52.781 602 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.40 % Allowed : 19.61 % Favored : 78.00 % 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: 1.52 (0.36), residues: 536 helix: 1.63 (0.30), residues: 301 sheet: -0.27 (0.74), residues: 43 loop : 0.50 (0.46), residues: 192 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 636 TYR 0.008 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 *********************** 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 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.496 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 35 average time/residue: 1.1603 time to fit residues: 42.8470 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 : 0.537 ------------------------------------------------------------------------------- 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 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4401 Z= 0.207 Angle : 0.515 8.221 5957 Z= 0.264 Chirality : 0.041 0.143 650 Planarity : 0.003 0.030 779 Dihedral : 6.103 53.361 602 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 20.26 % Favored : 77.78 % 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: 1.50 (0.36), residues: 536 helix: 1.60 (0.30), residues: 301 sheet: -0.30 (0.73), residues: 43 loop : 0.50 (0.45), residues: 192 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 636 TYR 0.008 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 ********************** 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 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.525 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 34 average time/residue: 1.1273 time to fit residues: 40.4217 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 : 0.517 ------------------------------------------------------------------------------- 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 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** 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 = 0.3229 r_free = 0.3229 target = 0.054301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048439 restraints weight = 15708.222| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.98 r_work: 0.2941 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4401 Z= 0.184 Angle : 0.508 8.593 5957 Z= 0.259 Chirality : 0.041 0.140 650 Planarity : 0.003 0.030 779 Dihedral : 6.068 54.364 602 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 20.26 % Favored : 77.78 % 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: 1.54 (0.36), residues: 536 helix: 1.64 (0.30), residues: 301 sheet: -0.31 (0.73), residues: 43 loop : 0.52 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.008 0.001 PHE A 879 TYR 0.007 0.001 TYR A 680 ARG 0.002 0.000 ARG A 845 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.80 seconds wall clock time: 30 minutes 15.93 seconds (1815.93 seconds total)