Starting phenix.real_space_refine on Fri Jul 3 15:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9k_15934/07_2026/8b9k_15934.map" } resolution = 4.04 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 Anisotropic ADP refinement not supported. Converting 7434 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 42 5.49 5 S 47 5.16 5 C 5161 2.51 5 N 1447 2.21 5 O 1688 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.17s 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: 8390 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7511 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 951, 7500 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 951, 7500 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 7633 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 847 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 37} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.39 Number of scatterers: 8390 At special positions: 0 Unit cell: (73.98, 106.038, 139.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 42 15.00 Al 1 13.00 F 4 9.00 O 1688 8.00 N 1447 7.00 C 5161 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 585.5 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 47.3% alpha, 10.4% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.157A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.681A pdb=" N ILE A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.316A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 513 through 530 removed outlier: 3.905A pdb=" N ASP A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.510A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.527A pdb=" N ASP A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.085A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.778A pdb=" N GLN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.828A pdb=" N GLU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 722' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.897A pdb=" N ALA A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 removed outlier: 3.891A pdb=" N VAL A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.619A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 4.405A pdb=" N MET A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 939 through 950 removed outlier: 3.668A pdb=" N GLU A 943 " --> pdb=" O GLY A 939 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 975 Processing helix chain 'A' and resid 994 through 1008 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 4.235A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.713A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.604A pdb=" N CYS A 341 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 removed outlier: 6.545A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.339A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN A 686 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 715 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 688 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 743 removed outlier: 4.192A pdb=" N ALA A 753 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1054 through 1056 removed outlier: 8.220A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1082 through 1085 removed outlier: 3.619A pdb=" N ILE A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.04 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: 2569 1.34 - 1.46: 1381 1.46 - 1.57: 4529 1.57 - 1.69: 82 1.69 - 1.81: 75 Bond restraints: 8636 Sorted by residual: bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.48e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 8631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.19: 11891 14.19 - 28.38: 4 28.38 - 42.57: 0 42.57 - 56.76: 0 56.76 - 70.95: 2 Bond angle restraints: 11897 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 179.63 -70.95 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.62 -69.99 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 89.38 20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.36 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 89.66 19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 11892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 4827 20.48 - 40.95: 288 40.95 - 61.43: 58 61.43 - 81.91: 7 81.91 - 102.38: 6 Dihedral angle restraints: 5186 sinusoidal: 2393 harmonic: 2793 Sorted by residual: dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -162.38 102.38 1 2.00e+01 2.50e-03 2.91e+01 dihedral pdb=" CA TYR A 263 " pdb=" C TYR A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA MET A 629 " pdb=" C MET A 629 " pdb=" N LEU A 630 " pdb=" CA LEU A 630 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 868 0.027 - 0.054: 328 0.054 - 0.081: 103 0.081 - 0.108: 74 0.108 - 0.135: 22 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA VAL A 559 " pdb=" N VAL A 559 " pdb=" C VAL A 559 " pdb=" CB VAL A 559 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA PRO A 385 " pdb=" N PRO A 385 " pdb=" C PRO A 385 " pdb=" CB PRO A 385 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A 542 " pdb=" N ILE A 542 " pdb=" C ILE A 542 " pdb=" CB ILE A 542 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1392 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 440 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 441 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 390 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ARG A 390 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 390 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A1009 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A1010 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1010 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1010 " 0.020 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 376 2.71 - 3.26: 9101 3.26 - 3.80: 14735 3.80 - 4.35: 17695 4.35 - 4.90: 27573 Nonbonded interactions: 69480 Sorted by model distance: nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.160 3.040 nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.163 3.040 nonbonded pdb=" OD2 ASP A 993 " pdb=" OG SER A1150 " model vdw 2.195 3.040 nonbonded pdb=" O3B ADP A1201 " pdb=" F1 ALF A1202 " model vdw 2.201 2.990 nonbonded pdb=" OE1 GLU A 459 " pdb=" OG1 THR A 464 " model vdw 2.209 3.040 ... (remaining 69475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.260 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 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 0.100 8637 Z= 0.185 Angle : 1.152 70.945 11897 Z= 0.460 Chirality : 0.039 0.135 1395 Planarity : 0.004 0.058 1381 Dihedral : 13.419 102.381 3368 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.48 % Favored : 88.89 % Rotamer: Outliers : 5.04 % Allowed : 10.79 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.89 (0.29), residues: 947 helix: 0.99 (0.26), residues: 413 sheet: -1.34 (0.42), residues: 157 loop : -2.06 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.008 0.001 TYR A 467 PHE 0.007 0.001 PHE A 475 TRP 0.006 0.001 TRP A 328 HIS 0.002 0.000 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 ( 8636) covalent geometry : angle 1.15237 / 0.46 (11897) hydrogen bonds : bond 0.12791 / 8.52 ( 376) hydrogen bonds : angle 5.18261 / 3.51 ( 1040) Misc. bond : bond 0.00319 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7333 (mmp80) REVERT: A 602 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6463 (pm20) REVERT: A 1003 LEU cc_start: 0.8438 (mt) cc_final: 0.7818 (mt) outliers start: 40 outliers final: 9 residues processed: 141 average time/residue: 0.0846 time to fit residues: 17.1893 Evaluate side-chains 78 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.063582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.041610 restraints weight = 184935.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043473 restraints weight = 98640.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.044963 restraints weight = 66863.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.045891 restraints weight = 50776.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.046549 restraints weight = 41949.819| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8637 Z= 0.163 Angle : 0.768 12.557 11897 Z= 0.369 Chirality : 0.046 0.437 1395 Planarity : 0.005 0.044 1381 Dihedral : 9.597 90.043 1516 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.95 % Favored : 89.74 % Rotamer: Outliers : 0.24 % Allowed : 1.08 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.14 (0.28), residues: 947 helix: 0.53 (0.24), residues: 420 sheet: -1.20 (0.43), residues: 150 loop : -2.02 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 492 TYR 0.009 0.001 TYR A 752 PHE 0.017 0.002 PHE A1045 TRP 0.029 0.002 TRP A 328 HIS 0.011 0.002 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8636) covalent geometry : angle 0.76818 / 0.37 (11897) hydrogen bonds : bond 0.04788 / 3.12 ( 376) hydrogen bonds : angle 4.75967 / 3.26 ( 1040) Misc. bond : bond 0.00286 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8819 (pmm) cc_final: 0.8508 (pmm) REVERT: A 483 LEU cc_start: 0.8980 (tp) cc_final: 0.8764 (tp) REVERT: A 543 ASP cc_start: 0.8934 (p0) cc_final: 0.8189 (p0) REVERT: A 756 TRP cc_start: 0.8409 (m100) cc_final: 0.8089 (m100) REVERT: A 898 PHE cc_start: 0.8881 (m-80) cc_final: 0.8297 (m-80) REVERT: A 922 HIS cc_start: 0.8501 (m90) cc_final: 0.8212 (m-70) REVERT: A 1047 TYR cc_start: 0.8429 (m-80) cc_final: 0.7915 (m-80) REVERT: A 1153 ASP cc_start: 0.9066 (m-30) cc_final: 0.8286 (t0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0803 time to fit residues: 11.2225 Evaluate side-chains 71 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 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 = 0.3706 r_free = 0.3706 target = 0.062501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.041768 restraints weight = 138053.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.043442 restraints weight = 82825.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044576 restraints weight = 59317.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.045441 restraints weight = 46710.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.046042 restraints weight = 39114.462| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8637 Z= 0.156 Angle : 0.718 10.815 11897 Z= 0.347 Chirality : 0.044 0.325 1395 Planarity : 0.004 0.038 1381 Dihedral : 9.493 90.472 1516 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.74 % Favored : 89.95 % Rotamer: Outliers : 0.24 % Allowed : 1.80 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.21 (0.28), residues: 947 helix: 0.45 (0.24), residues: 425 sheet: -1.26 (0.42), residues: 151 loop : -2.05 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 492 TYR 0.018 0.001 TYR A 420 PHE 0.014 0.001 PHE A1045 TRP 0.029 0.002 TRP A 328 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 8636) covalent geometry : angle 0.71792 / 0.35 (11897) hydrogen bonds : bond 0.04486 / 2.97 ( 376) hydrogen bonds : angle 4.75820 / 3.27 ( 1040) Misc. bond : bond 0.00251 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8881 (pmm) cc_final: 0.8569 (pmm) REVERT: A 543 ASP cc_start: 0.8968 (p0) cc_final: 0.8274 (p0) REVERT: A 629 MET cc_start: 0.7583 (pmm) cc_final: 0.7222 (tpt) REVERT: A 756 TRP cc_start: 0.8457 (m100) cc_final: 0.8141 (m100) REVERT: A 807 LEU cc_start: 0.9483 (mt) cc_final: 0.9189 (tt) REVERT: A 887 MET cc_start: 0.8871 (ppp) cc_final: 0.8649 (ppp) REVERT: A 898 PHE cc_start: 0.8810 (m-80) cc_final: 0.8392 (m-80) REVERT: A 922 HIS cc_start: 0.8795 (m90) cc_final: 0.8442 (m-70) REVERT: A 957 MET cc_start: 0.9551 (ttt) cc_final: 0.9206 (tmm) REVERT: A 1153 ASP cc_start: 0.9106 (m-30) cc_final: 0.8339 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0724 time to fit residues: 8.9899 Evaluate side-chains 66 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.061882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.040415 restraints weight = 177747.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.042283 restraints weight = 96611.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043624 restraints weight = 66583.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.044618 restraints weight = 51042.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.045235 restraints weight = 41817.276| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8637 Z= 0.142 Angle : 0.687 10.390 11897 Z= 0.333 Chirality : 0.043 0.324 1395 Planarity : 0.004 0.035 1381 Dihedral : 9.471 90.794 1516 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.21 % Favored : 90.37 % Rotamer: Outliers : 0.24 % Allowed : 1.80 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.18 (0.28), residues: 947 helix: 0.51 (0.25), residues: 425 sheet: -1.32 (0.42), residues: 142 loop : -2.04 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.010 0.001 TYR A 420 PHE 0.011 0.001 PHE A 878 TRP 0.020 0.002 TRP A 328 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8636) covalent geometry : angle 0.68663 / 0.33 (11897) hydrogen bonds : bond 0.04262 / 2.80 ( 376) hydrogen bonds : angle 4.68118 / 3.22 ( 1040) Misc. bond : bond 0.00264 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8960 (pmm) cc_final: 0.8669 (pmm) REVERT: A 543 ASP cc_start: 0.9094 (p0) cc_final: 0.8407 (p0) REVERT: A 629 MET cc_start: 0.7536 (pmm) cc_final: 0.7316 (tpt) REVERT: A 756 TRP cc_start: 0.8515 (m100) cc_final: 0.8209 (m100) REVERT: A 807 LEU cc_start: 0.9497 (mt) cc_final: 0.9210 (tt) REVERT: A 922 HIS cc_start: 0.8878 (m90) cc_final: 0.8486 (m-70) REVERT: A 957 MET cc_start: 0.9570 (ttt) cc_final: 0.9226 (tmm) REVERT: A 1153 ASP cc_start: 0.9207 (m-30) cc_final: 0.8401 (t0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0788 time to fit residues: 9.0548 Evaluate side-chains 61 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.0020 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.062792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.040949 restraints weight = 199533.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.042991 restraints weight = 101644.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.044422 restraints weight = 67880.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.045384 restraints weight = 51271.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.046087 restraints weight = 41721.011| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8637 Z= 0.125 Angle : 0.675 10.573 11897 Z= 0.326 Chirality : 0.043 0.309 1395 Planarity : 0.004 0.036 1381 Dihedral : 9.379 90.342 1516 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.78 % Favored : 90.79 % Rotamer: Outliers : 0.24 % Allowed : 2.04 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.15 (0.28), residues: 947 helix: 0.53 (0.25), residues: 424 sheet: -1.29 (0.42), residues: 142 loop : -2.03 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.011 0.001 TYR A 420 PHE 0.010 0.001 PHE A 786 TRP 0.017 0.001 TRP A 961 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8636) covalent geometry : angle 0.67521 / 0.33 (11897) hydrogen bonds : bond 0.04038 / 2.66 ( 376) hydrogen bonds : angle 4.60468 / 3.18 ( 1040) Misc. bond : bond 0.00238 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9080 (p0) cc_final: 0.8439 (p0) REVERT: A 756 TRP cc_start: 0.8473 (m100) cc_final: 0.8182 (m100) REVERT: A 807 LEU cc_start: 0.9480 (mt) cc_final: 0.9198 (tt) REVERT: A 898 PHE cc_start: 0.8526 (m-80) cc_final: 0.8189 (m-80) REVERT: A 922 HIS cc_start: 0.8900 (m90) cc_final: 0.8535 (m-70) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0746 time to fit residues: 8.6615 Evaluate side-chains 66 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 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 = 0.3745 r_free = 0.3745 target = 0.063049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.041536 restraints weight = 187131.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.043641 restraints weight = 97014.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.045041 restraints weight = 64838.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.046016 restraints weight = 49385.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.046708 restraints weight = 40203.114| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8637 Z= 0.119 Angle : 0.676 12.398 11897 Z= 0.325 Chirality : 0.043 0.363 1395 Planarity : 0.004 0.036 1381 Dihedral : 9.212 89.612 1516 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.78 % Favored : 90.90 % Rotamer: Outliers : 0.24 % Allowed : 1.08 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.10 (0.28), residues: 947 helix: 0.52 (0.25), residues: 425 sheet: -1.30 (0.42), residues: 143 loop : -1.91 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.014 0.001 TYR A 437 PHE 0.009 0.001 PHE A 786 TRP 0.017 0.001 TRP A 961 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8636) covalent geometry : angle 0.67647 / 0.33 (11897) hydrogen bonds : bond 0.03881 / 2.53 ( 376) hydrogen bonds : angle 4.49617 / 3.12 ( 1040) Misc. bond : bond 0.00252 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9073 (p0) cc_final: 0.8425 (p0) REVERT: A 756 TRP cc_start: 0.8445 (m100) cc_final: 0.8136 (m100) REVERT: A 807 LEU cc_start: 0.9485 (mt) cc_final: 0.9200 (tt) REVERT: A 887 MET cc_start: 0.8747 (ppp) cc_final: 0.8547 (ppp) REVERT: A 922 HIS cc_start: 0.8937 (m90) cc_final: 0.8592 (m-70) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0789 time to fit residues: 9.5692 Evaluate side-chains 67 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.1980 chunk 47 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 HIS ** A 966 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 = 0.3751 r_free = 0.3751 target = 0.062571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.041567 restraints weight = 187906.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.043606 restraints weight = 96488.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044936 restraints weight = 63895.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.045825 restraints weight = 48427.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.046564 restraints weight = 40036.051| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8637 Z= 0.123 Angle : 0.672 10.367 11897 Z= 0.324 Chirality : 0.043 0.362 1395 Planarity : 0.004 0.035 1381 Dihedral : 9.074 88.829 1516 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.68 % Favored : 91.01 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.03 (0.28), residues: 947 helix: 0.55 (0.25), residues: 425 sheet: -1.27 (0.42), residues: 143 loop : -1.84 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.009 0.001 TYR A 437 PHE 0.011 0.001 PHE A1077 TRP 0.024 0.002 TRP A 961 HIS 0.003 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8636) covalent geometry : angle 0.67217 / 0.32 (11897) hydrogen bonds : bond 0.03846 / 2.53 ( 376) hydrogen bonds : angle 4.53992 / 3.15 ( 1040) Misc. bond : bond 0.00253 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9055 (p0) cc_final: 0.8437 (p0) REVERT: A 756 TRP cc_start: 0.8424 (m100) cc_final: 0.8100 (m100) REVERT: A 807 LEU cc_start: 0.9489 (mt) cc_final: 0.9207 (tt) REVERT: A 922 HIS cc_start: 0.8943 (m90) cc_final: 0.8645 (m-70) REVERT: A 1063 CYS cc_start: 0.7350 (p) cc_final: 0.6694 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0761 time to fit residues: 8.7105 Evaluate side-chains 64 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.061980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041417 restraints weight = 168011.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.043269 restraints weight = 90912.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.044556 restraints weight = 61671.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.045407 restraints weight = 47031.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.046149 restraints weight = 38933.406| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8637 Z= 0.127 Angle : 0.665 9.977 11897 Z= 0.322 Chirality : 0.043 0.372 1395 Planarity : 0.004 0.034 1381 Dihedral : 9.006 88.396 1516 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.31 % Favored : 90.37 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.94 (0.28), residues: 947 helix: 0.60 (0.25), residues: 427 sheet: -1.27 (0.42), residues: 143 loop : -1.76 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.009 0.001 TYR A 177 PHE 0.008 0.001 PHE A 786 TRP 0.023 0.002 TRP A 961 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8636) covalent geometry : angle 0.66546 / 0.32 (11897) hydrogen bonds : bond 0.03880 / 2.56 ( 376) hydrogen bonds : angle 4.57439 / 3.17 ( 1040) Misc. bond : bond 0.00260 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9073 (p0) cc_final: 0.8432 (p0) REVERT: A 756 TRP cc_start: 0.8438 (m100) cc_final: 0.8024 (m100) REVERT: A 807 LEU cc_start: 0.9497 (mt) cc_final: 0.9221 (tt) REVERT: A 922 HIS cc_start: 0.8975 (m90) cc_final: 0.8597 (m-70) REVERT: A 1063 CYS cc_start: 0.7558 (p) cc_final: 0.6824 (m) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0824 time to fit residues: 8.8957 Evaluate side-chains 61 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.0050 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.061925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.040744 restraints weight = 214765.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.042875 restraints weight = 104263.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044264 restraints weight = 67189.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.045256 restraints weight = 50019.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.045941 restraints weight = 40576.588| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8637 Z= 0.127 Angle : 0.683 11.751 11897 Z= 0.330 Chirality : 0.043 0.353 1395 Planarity : 0.004 0.035 1381 Dihedral : 9.037 88.254 1516 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.10 % Favored : 90.58 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.28), residues: 947 helix: 0.59 (0.25), residues: 427 sheet: -1.36 (0.41), residues: 146 loop : -1.74 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.008 0.001 TYR A 177 PHE 0.013 0.001 PHE A 240 TRP 0.049 0.003 TRP A 165 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8636) covalent geometry : angle 0.68266 / 0.33 (11897) hydrogen bonds : bond 0.03802 / 2.51 ( 376) hydrogen bonds : angle 4.60950 / 3.20 ( 1040) Misc. bond : bond 0.00249 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9091 (p0) cc_final: 0.8446 (p0) REVERT: A 756 TRP cc_start: 0.8437 (m100) cc_final: 0.8011 (m100) REVERT: A 807 LEU cc_start: 0.9505 (mt) cc_final: 0.9233 (tt) REVERT: A 922 HIS cc_start: 0.8973 (m90) cc_final: 0.8629 (m-70) REVERT: A 1063 CYS cc_start: 0.7448 (p) cc_final: 0.6643 (m) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0708 time to fit residues: 7.9613 Evaluate side-chains 62 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 chunk 96 optimal weight: 10.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.0020 chunk 90 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 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 = 0.3653 r_free = 0.3653 target = 0.059310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.038831 restraints weight = 180017.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.040629 restraints weight = 99924.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.041955 restraints weight = 68422.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.042780 restraints weight = 52365.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.043290 restraints weight = 43566.603| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8637 Z= 0.184 Angle : 0.737 11.500 11897 Z= 0.361 Chirality : 0.045 0.367 1395 Planarity : 0.004 0.039 1381 Dihedral : 9.415 89.243 1516 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.74 % Favored : 89.95 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.16 (0.28), residues: 947 helix: 0.40 (0.24), residues: 431 sheet: -1.46 (0.41), residues: 147 loop : -1.81 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 696 TYR 0.014 0.001 TYR A1009 PHE 0.011 0.002 PHE A1077 TRP 0.042 0.003 TRP A 165 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 8636) covalent geometry : angle 0.73667 / 0.36 (11897) hydrogen bonds : bond 0.04697 / 3.10 ( 376) hydrogen bonds : angle 4.86530 / 3.38 ( 1040) Misc. bond : bond 0.00257 / 0.14 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9167 (p0) cc_final: 0.8861 (p0) REVERT: A 887 MET cc_start: 0.9032 (ppp) cc_final: 0.8763 (ppp) REVERT: A 1003 LEU cc_start: 0.9095 (mt) cc_final: 0.8893 (mt) REVERT: A 1047 TYR cc_start: 0.8267 (m-80) cc_final: 0.7632 (m-80) REVERT: A 1063 CYS cc_start: 0.7316 (p) cc_final: 0.6514 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0820 time to fit residues: 8.7327 Evaluate side-chains 59 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 77 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.062322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.042322 restraints weight = 139624.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.044033 restraints weight = 79954.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.045217 restraints weight = 56060.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.046041 restraints weight = 43560.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.046657 restraints weight = 36538.024| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8637 Z= 0.121 Angle : 0.692 11.762 11897 Z= 0.334 Chirality : 0.044 0.374 1395 Planarity : 0.004 0.058 1381 Dihedral : 9.200 89.381 1516 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.94 % Favored : 91.64 % Rotamer: Outliers : 0.24 % Allowed : 0.12 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.08 (0.27), residues: 947 helix: 0.51 (0.25), residues: 428 sheet: -1.66 (0.42), residues: 130 loop : -1.72 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1158 TYR 0.010 0.001 TYR A 420 PHE 0.020 0.001 PHE A1077 TRP 0.043 0.003 TRP A 756 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8636) covalent geometry : angle 0.69187 / 0.33 (11897) hydrogen bonds : bond 0.03733 / 2.44 ( 376) hydrogen bonds : angle 4.58803 / 3.19 ( 1040) Misc. bond : bond 0.00263 / 0.14 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.94 seconds wall clock time: 38 minutes 38.68 seconds (2318.68 seconds total)