Starting phenix.real_space_refine on Thu Aug 6 10:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9k_15934/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2026/8b9k_15934.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: {'RNAv2': 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: 3.19, per 1000 atoms: 0.38 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: 0.65 Conformation dependent library (CDL) restraints added in 510.1 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: 1.40 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: 1.92 Time building geometry restraints manager: 0.85 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: 4775 20.48 - 40.95: 310 40.95 - 61.43: 87 61.43 - 81.91: 9 81.91 - 102.38: 5 Dihedral angle restraints: 5186 sinusoidal: 2393 harmonic: 2793 Sorted by residual: dihedral pdb=" C4' C B 44 " pdb=" C3' C B 44 " pdb=" C2' C B 44 " pdb=" C1' C B 44 " ideal model delta sinusoidal sigma weight residual 36.34 -37.10 73.44 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' C B 45 " pdb=" C3' C B 45 " pdb=" C2' C B 45 " pdb=" C1' C B 45 " ideal model delta sinusoidal sigma weight residual 36.34 -35.58 71.92 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' C B 46 " pdb=" C3' C B 46 " pdb=" C2' C B 46 " pdb=" C1' C B 46 " ideal model delta sinusoidal sigma weight residual 36.34 -35.22 71.57 1 3.10e+00 1.04e-01 6.83e+02 ... (remaining 5183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1155 0.055 - 0.110: 178 0.110 - 0.166: 16 0.166 - 0.221: 2 0.221 - 0.276: 44 Chirality restraints: 1395 Sorted by residual: chirality pdb=" C3' C B 44 " pdb=" C4' C B 44 " pdb=" O3' C B 44 " pdb=" C2' C B 44 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' C B 45 " pdb=" C3' C B 45 " pdb=" O2' C B 45 " pdb=" C1' C B 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' C B 46 " pdb=" C3' C B 46 " pdb=" O2' C B 46 " pdb=" C1' C B 46 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (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: 3.250 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- 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= 0.188 Angle : 1.185 70.945 11897 Z= 0.468 Chirality : 0.058 0.276 1395 Planarity : 0.004 0.058 1381 Dihedral : 14.507 102.381 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 0.00363 / 0.19 ( 8636) covalent geometry : angle 1.18479 / 0.47 (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 : 0.305 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: 0.0800 time to fit residues: 16.2832 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 : 0.299 ------------------------------------------------------------------------------- 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: 9.9990 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 A 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.041983 restraints weight = 184328.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.043921 restraints weight = 97565.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.045368 restraints weight = 65842.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.046410 restraints weight = 49920.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.047097 restraints weight = 40844.634| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 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 = 0.3292 r_free = 0.3292 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: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1934 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= 0.160 Angle : 0.883 22.091 11897 Z= 0.395 Chirality : 0.074 1.484 1395 Planarity : 0.005 0.044 1381 Dihedral : 11.057 68.367 1516 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.74 % Favored : 89.95 % 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: -1.15 (0.28), residues: 947 helix: 0.51 (0.24), residues: 420 sheet: -1.23 (0.43), residues: 151 loop : -2.01 (0.34), residues: 376 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 0.018 0.002 PHE A1045 TRP 0.030 0.002 TRP A 328 HIS 0.011 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8636) covalent geometry : angle 0.88318 / 0.40 (11897) hydrogen bonds : bond 0.04773 / 3.09 ( 376) hydrogen bonds : angle 4.76379 / 3.26 ( 1040) Misc. bond : bond 0.00295 / 0.16 ( 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 95 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8847 (pmm) cc_final: 0.8540 (pmm) REVERT: A 483 LEU cc_start: 0.8963 (tp) cc_final: 0.8750 (tp) REVERT: A 543 ASP cc_start: 0.8940 (p0) cc_final: 0.8203 (p0) REVERT: A 756 TRP cc_start: 0.8389 (m100) cc_final: 0.8052 (m100) REVERT: A 898 PHE cc_start: 0.8883 (m-80) cc_final: 0.8482 (m-80) REVERT: A 922 HIS cc_start: 0.8560 (m90) cc_final: 0.8268 (m-70) REVERT: A 1047 TYR cc_start: 0.8471 (m-80) cc_final: 0.8098 (m-80) REVERT: A 1153 ASP cc_start: 0.9110 (m-30) cc_final: 0.8312 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0777 time to fit residues: 11.0450 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 : 0.304 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.063376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.042395 restraints weight = 136373.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044134 restraints weight = 82079.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.045326 restraints weight = 58524.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.046162 restraints weight = 46122.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.046782 restraints weight = 38531.524| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 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 = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2489 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= 0.141 Angle : 0.794 16.660 11897 Z= 0.359 Chirality : 0.059 1.131 1395 Planarity : 0.004 0.037 1381 Dihedral : 10.456 59.492 1516 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.52 % Favored : 90.16 % Rotamer: Outliers : 0.24 % Allowed : 1.44 % Favored : 98.32 % 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: -1.20 (0.28), residues: 947 helix: 0.45 (0.24), residues: 425 sheet: -1.20 (0.42), residues: 151 loop : -2.07 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 492 TYR 0.019 0.001 TYR A 420 PHE 0.010 0.001 PHE A 976 TRP 0.028 0.002 TRP A 328 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8636) covalent geometry : angle 0.79421 / 0.36 (11897) hydrogen bonds : bond 0.04345 / 2.87 ( 376) hydrogen bonds : angle 4.68597 / 3.22 ( 1040) Misc. bond : bond 0.00264 / 0.14 ( 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 87 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8881 (pmm) cc_final: 0.8574 (pmm) REVERT: A 543 ASP cc_start: 0.8980 (p0) cc_final: 0.8344 (p0) REVERT: A 629 MET cc_start: 0.7632 (pmm) cc_final: 0.7202 (tpt) REVERT: A 756 TRP cc_start: 0.8486 (m100) cc_final: 0.8110 (m100) REVERT: A 807 LEU cc_start: 0.9468 (mt) cc_final: 0.9151 (tt) REVERT: A 887 MET cc_start: 0.8827 (ppp) cc_final: 0.8586 (ppp) REVERT: A 898 PHE cc_start: 0.8750 (m-80) cc_final: 0.8325 (m-80) REVERT: A 922 HIS cc_start: 0.8783 (m90) cc_final: 0.8440 (m-70) REVERT: A 957 MET cc_start: 0.9517 (ttt) cc_final: 0.9227 (tmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0774 time to fit residues: 9.9924 Evaluate side-chains 68 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 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 = 0.3637 r_free = 0.3637 target = 0.059418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.038755 restraints weight = 183105.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040484 restraints weight = 99224.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.041757 restraints weight = 68117.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.042622 restraints weight = 52648.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.043222 restraints weight = 43604.232| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8637 Z= 0.236 Angle : 0.862 15.584 11897 Z= 0.400 Chirality : 0.057 0.909 1395 Planarity : 0.005 0.041 1381 Dihedral : 10.594 61.708 1516 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.84 % Favored : 89.74 % 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: -1.54 (0.27), residues: 947 helix: 0.15 (0.24), residues: 427 sheet: -1.45 (0.40), residues: 155 loop : -2.20 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 739 TYR 0.015 0.002 TYR A 263 PHE 0.018 0.002 PHE A 976 TRP 0.023 0.002 TRP A 328 HIS 0.007 0.002 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.24 ( 8636) covalent geometry : angle 0.86183 / 0.40 (11897) hydrogen bonds : bond 0.05504 / 3.64 ( 376) hydrogen bonds : angle 5.08250 / 3.50 ( 1040) Misc. bond : bond 0.00277 / 0.15 ( 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 73 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8943 (pmm) cc_final: 0.8660 (pmm) REVERT: A 543 ASP cc_start: 0.9105 (p0) cc_final: 0.8771 (p0) REVERT: A 629 MET cc_start: 0.7528 (pmm) cc_final: 0.7265 (tpt) REVERT: A 807 LEU cc_start: 0.9511 (mt) cc_final: 0.9269 (tt) REVERT: A 887 MET cc_start: 0.9031 (ppp) cc_final: 0.8798 (ppp) REVERT: A 898 PHE cc_start: 0.8799 (m-80) cc_final: 0.8190 (m-80) REVERT: A 922 HIS cc_start: 0.8852 (m90) cc_final: 0.8480 (m-70) REVERT: A 957 MET cc_start: 0.9588 (ttt) cc_final: 0.9130 (tmm) REVERT: A 1063 CYS cc_start: 0.7548 (p) cc_final: 0.6983 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0760 time to fit residues: 8.3823 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.0770 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.061938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.040373 restraints weight = 204566.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.042339 restraints weight = 103879.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.043803 restraints weight = 69186.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.044768 restraints weight = 52303.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.045495 restraints weight = 42963.622| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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 = 0.3263 r_free = 0.3263 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: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8637 Z= 0.131 Angle : 0.771 14.731 11897 Z= 0.353 Chirality : 0.055 0.949 1395 Planarity : 0.004 0.038 1381 Dihedral : 10.446 61.079 1516 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.89 % Favored : 90.58 % Rotamer: Outliers : 0.24 % Allowed : 1.92 % Favored : 97.84 % 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: -1.27 (0.28), residues: 947 helix: 0.42 (0.25), residues: 424 sheet: -1.46 (0.41), residues: 142 loop : -2.03 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.010 0.001 TYR A 420 PHE 0.010 0.001 PHE A 786 TRP 0.030 0.002 TRP A 756 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8636) covalent geometry : angle 0.77058 / 0.35 (11897) hydrogen bonds : bond 0.04199 / 2.77 ( 376) hydrogen bonds : angle 4.73900 / 3.27 ( 1040) Misc. bond : bond 0.00282 / 0.15 ( 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 76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9042 (p0) cc_final: 0.8414 (p0) REVERT: A 807 LEU cc_start: 0.9505 (mt) cc_final: 0.9237 (tt) REVERT: A 887 MET cc_start: 0.8888 (ppp) cc_final: 0.8681 (ppp) REVERT: A 898 PHE cc_start: 0.8685 (m-80) cc_final: 0.8241 (m-80) REVERT: A 922 HIS cc_start: 0.8832 (m90) cc_final: 0.8461 (m-70) REVERT: A 957 MET cc_start: 0.9503 (ttt) cc_final: 0.9113 (tmm) REVERT: A 1063 CYS cc_start: 0.7347 (p) cc_final: 0.6753 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0710 time to fit residues: 8.3853 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 : 0.278 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.062195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.040968 restraints weight = 191960.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.042992 restraints weight = 99666.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.044428 restraints weight = 66707.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.045393 restraints weight = 50668.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.046104 restraints weight = 41401.563| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 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 = 0.3267 r_free = 0.3267 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: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3267 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= 0.128 Angle : 0.756 14.509 11897 Z= 0.344 Chirality : 0.054 0.918 1395 Planarity : 0.004 0.037 1381 Dihedral : 10.398 62.066 1516 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.10 % Favored : 90.58 % 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: -1.20 (0.28), residues: 947 helix: 0.42 (0.25), residues: 425 sheet: -1.40 (0.41), residues: 143 loop : -1.92 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.013 0.001 TYR A 437 PHE 0.025 0.001 PHE A 240 TRP 0.046 0.003 TRP A 165 HIS 0.003 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8636) covalent geometry : angle 0.75554 / 0.34 (11897) hydrogen bonds : bond 0.04058 / 2.68 ( 376) hydrogen bonds : angle 4.68484 / 3.26 ( 1040) Misc. bond : bond 0.00268 / 0.14 ( 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 76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9086 (p0) cc_final: 0.8394 (p0) REVERT: A 756 TRP cc_start: 0.8253 (m100) cc_final: 0.7826 (m100) REVERT: A 807 LEU cc_start: 0.9500 (mt) cc_final: 0.9227 (tt) REVERT: A 887 MET cc_start: 0.8820 (ppp) cc_final: 0.8585 (ppp) REVERT: A 922 HIS cc_start: 0.8888 (m90) cc_final: 0.8567 (m-70) REVERT: A 957 MET cc_start: 0.9494 (ttt) cc_final: 0.9116 (tmm) REVERT: A 1063 CYS cc_start: 0.7358 (p) cc_final: 0.6703 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0706 time to fit residues: 8.3060 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 : 0.302 ------------------------------------------------------------------------------- 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: 9.9990 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 40.0000 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.060524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039451 restraints weight = 190975.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.041302 restraints weight = 101607.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.042659 restraints weight = 69323.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.043629 restraints weight = 52742.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.044265 restraints weight = 43434.901| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3486 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= 0.156 Angle : 0.767 14.478 11897 Z= 0.352 Chirality : 0.054 0.905 1395 Planarity : 0.004 0.036 1381 Dihedral : 10.372 62.165 1516 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.21 % Favored : 90.48 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % 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: -1.22 (0.28), residues: 947 helix: 0.45 (0.25), residues: 428 sheet: -1.41 (0.42), residues: 128 loop : -2.02 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.009 0.001 TYR A 437 PHE 0.011 0.001 PHE A 898 TRP 0.026 0.002 TRP A 165 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 8636) covalent geometry : angle 0.76662 / 0.35 (11897) hydrogen bonds : bond 0.04348 / 2.85 ( 376) hydrogen bonds : angle 4.73700 / 3.27 ( 1040) Misc. bond : bond 0.00263 / 0.14 ( 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 73 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9149 (p0) cc_final: 0.8462 (p0) REVERT: A 807 LEU cc_start: 0.9524 (mt) cc_final: 0.9269 (tt) REVERT: A 887 MET cc_start: 0.8955 (ppp) cc_final: 0.8741 (ppp) REVERT: A 898 PHE cc_start: 0.8500 (m-80) cc_final: 0.8072 (m-80) REVERT: A 922 HIS cc_start: 0.8915 (m90) cc_final: 0.8512 (m-70) REVERT: A 957 MET cc_start: 0.9513 (ttt) cc_final: 0.9161 (tmm) REVERT: A 1063 CYS cc_start: 0.7343 (p) cc_final: 0.6682 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0731 time to fit residues: 8.0415 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 : 0.292 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1824 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.061302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.040725 restraints weight = 170027.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.042588 restraints weight = 93960.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.043867 restraints weight = 64392.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.044699 restraints weight = 49621.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045411 restraints weight = 41592.507| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 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 = 0.3249 r_free = 0.3249 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: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3616 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= 0.127 Angle : 0.747 14.575 11897 Z= 0.343 Chirality : 0.054 0.924 1395 Planarity : 0.005 0.098 1381 Dihedral : 10.338 62.352 1516 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.89 % Favored : 90.79 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % 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: -1.07 (0.27), residues: 947 helix: 0.49 (0.25), residues: 425 sheet: -0.92 (0.47), residues: 112 loop : -1.95 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 624 TYR 0.009 0.001 TYR A 177 PHE 0.010 0.001 PHE A 786 TRP 0.043 0.003 TRP A 756 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 0.74703 / 0.34 (11897) hydrogen bonds : bond 0.03982 / 2.60 ( 376) hydrogen bonds : angle 4.64941 / 3.23 ( 1040) Misc. bond : bond 0.00254 / 0.13 ( 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 : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9178 (p0) cc_final: 0.8504 (p0) REVERT: A 807 LEU cc_start: 0.9502 (mt) cc_final: 0.9244 (tt) REVERT: A 922 HIS cc_start: 0.8960 (m90) cc_final: 0.8583 (m-70) REVERT: A 957 MET cc_start: 0.9534 (ttt) cc_final: 0.9185 (tmm) REVERT: A 1063 CYS cc_start: 0.7386 (p) cc_final: 0.6573 (m) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0687 time to fit residues: 7.8693 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 : 0.317 ------------------------------------------------------------------------------- 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: 7.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.061582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.040234 restraints weight = 217363.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.042300 restraints weight = 109376.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043749 restraints weight = 71518.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.044811 restraints weight = 53521.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.045522 restraints weight = 43433.178| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 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: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3769 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= 0.124 Angle : 0.740 14.759 11897 Z= 0.342 Chirality : 0.054 0.944 1395 Planarity : 0.004 0.065 1381 Dihedral : 10.273 63.055 1516 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.42 % Favored : 90.26 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -1.11 (0.28), residues: 947 helix: 0.47 (0.25), residues: 427 sheet: -1.28 (0.43), residues: 129 loop : -1.89 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 624 TYR 0.009 0.001 TYR A 177 PHE 0.013 0.001 PHE A 518 TRP 0.036 0.003 TRP A 756 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8636) covalent geometry : angle 0.73966 / 0.34 (11897) hydrogen bonds : bond 0.03880 / 2.53 ( 376) hydrogen bonds : angle 4.65745 / 3.24 ( 1040) Misc. bond : bond 0.00253 / 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 72 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9169 (p0) cc_final: 0.8500 (p0) REVERT: A 807 LEU cc_start: 0.9501 (mt) cc_final: 0.9243 (tt) REVERT: A 922 HIS cc_start: 0.8990 (m90) cc_final: 0.8612 (m-70) REVERT: A 957 MET cc_start: 0.9518 (ttt) cc_final: 0.9112 (tmm) REVERT: A 1063 CYS cc_start: 0.7385 (p) cc_final: 0.6499 (m) REVERT: A 1153 ASP cc_start: 0.8971 (m-30) cc_final: 0.8632 (m-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0640 time to fit residues: 7.1605 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 : 0.295 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 958 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.060326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.039685 restraints weight = 179277.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.041588 restraints weight = 97578.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.042846 restraints weight = 66287.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043827 restraints weight = 51044.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.044435 restraints weight = 42148.034| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3855 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= 0.151 Angle : 0.751 14.975 11897 Z= 0.349 Chirality : 0.054 0.951 1395 Planarity : 0.004 0.064 1381 Dihedral : 10.247 62.874 1516 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.21 % Favored : 90.48 % 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: -1.04 (0.28), residues: 947 helix: 0.48 (0.25), residues: 429 sheet: -0.95 (0.46), residues: 112 loop : -1.89 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 624 TYR 0.010 0.001 TYR A1009 PHE 0.008 0.001 PHE A 518 TRP 0.033 0.003 TRP A 756 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8636) covalent geometry : angle 0.75083 / 0.35 (11897) hydrogen bonds : bond 0.04227 / 2.79 ( 376) hydrogen bonds : angle 4.74801 / 3.29 ( 1040) Misc. bond : bond 0.00261 / 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 71 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9188 (p0) cc_final: 0.8864 (p0) REVERT: A 807 LEU cc_start: 0.9520 (mt) cc_final: 0.9268 (tt) REVERT: A 922 HIS cc_start: 0.8920 (m90) cc_final: 0.8522 (m-70) REVERT: A 957 MET cc_start: 0.9494 (ttt) cc_final: 0.9061 (tmm) REVERT: A 1063 CYS cc_start: 0.7295 (p) cc_final: 0.6522 (m) REVERT: A 1153 ASP cc_start: 0.8973 (m-30) cc_final: 0.8610 (m-30) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0682 time to fit residues: 7.4822 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 : 0.293 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 5.9990 chunk 40 optimal weight: 0.0040 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3694 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.061144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.041244 restraints weight = 142241.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.042945 restraints weight = 83219.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.044183 restraints weight = 58408.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045103 restraints weight = 45824.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.045661 restraints weight = 37979.725| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 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 = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3948 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 : 0.734 15.144 11897 Z= 0.340 Chirality : 0.054 0.970 1395 Planarity : 0.004 0.059 1381 Dihedral : 10.227 62.994 1516 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.78 % Favored : 90.90 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % 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: -1.09 (0.28), residues: 947 helix: 0.49 (0.25), residues: 427 sheet: -1.30 (0.43), residues: 129 loop : -1.88 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.009 0.001 TYR A 177 PHE 0.008 0.001 PHE A 786 TRP 0.030 0.002 TRP A 756 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8636) covalent geometry : angle 0.73443 / 0.34 (11897) hydrogen bonds : bond 0.03981 / 2.62 ( 376) hydrogen bonds : angle 4.67056 / 3.26 ( 1040) Misc. bond : bond 0.00238 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.89 seconds wall clock time: 38 minutes 11.15 seconds (2291.15 seconds total)