Starting phenix.real_space_refine on Sat Aug 23 21:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_15934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_15934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_15934.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_15934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9k_15934/08_2025/8b9k_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-2.0-5787/lib/python3.9/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: 4.06, per 1000 atoms: 0.48 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: 0.79 Conformation dependent library (CDL) restraints added in 523.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 1.59 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: 4870 20.48 - 40.95: 315 40.95 - 61.43: 100 61.43 - 81.91: 33 81.91 - 102.38: 6 Dihedral angle restraints: 5324 sinusoidal: 2531 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 5321 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: 2.840 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: 0.040 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 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 : 15.724 102.381 3506 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 aren 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 covalent geometry : bond 0.00356 ( 8636) covalent geometry : angle 1.15237 (11897) hydrogen bonds : bond 0.12791 ( 376) hydrogen bonds : angle 5.18261 ( 1040) Misc. bond : bond 0.00319 ( 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 : 0.316 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: 0.0899 time to fit residues: 17.9040 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 : 0.309 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3713 r_free = 0.3713 target = 0.064034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.041606 restraints weight = 182636.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.043587 restraints weight = 98800.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.044991 restraints weight = 66723.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.046006 restraints weight = 51022.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.046678 restraints weight = 41811.898| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8637 Z= 0.157 Angle : 0.769 12.350 11897 Z= 0.368 Chirality : 0.046 0.431 1395 Planarity : 0.005 0.043 1381 Dihedral : 15.344 90.709 1654 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.46 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 aren not related in a simple way. whole: -1.14 (0.28), residues: 947 helix: 0.52 (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 0.018 0.002 PHE A1045 TRP 0.030 0.002 TRP A 328 HIS 0.011 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8636) covalent geometry : angle 0.76922 (11897) hydrogen bonds : bond 0.04764 ( 376) hydrogen bonds : angle 4.76017 ( 1040) Misc. bond : bond 0.00288 ( 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 : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8844 (pmm) cc_final: 0.8539 (pmm) REVERT: A 483 LEU cc_start: 0.8966 (tp) cc_final: 0.8753 (tp) REVERT: A 543 ASP cc_start: 0.8951 (p0) cc_final: 0.8224 (p0) REVERT: A 756 TRP cc_start: 0.8411 (m100) cc_final: 0.8078 (m100) REVERT: A 898 PHE cc_start: 0.8901 (m-80) cc_final: 0.8304 (m-80) REVERT: A 922 HIS cc_start: 0.8532 (m90) cc_final: 0.8245 (m-70) REVERT: A 1047 TYR cc_start: 0.8489 (m-80) cc_final: 0.7952 (m-80) REVERT: A 1153 ASP cc_start: 0.9128 (m-30) cc_final: 0.8317 (t0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0847 time to fit residues: 11.6530 Evaluate side-chains 70 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 7.9990 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.060943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.040623 restraints weight = 137366.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.042210 restraints weight = 82851.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.043346 restraints weight = 59241.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.044121 restraints weight = 46949.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.044714 restraints weight = 39677.075| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 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 = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8637 Z= 0.193 Angle : 0.747 10.318 11897 Z= 0.365 Chirality : 0.045 0.320 1395 Planarity : 0.005 0.042 1381 Dihedral : 15.432 91.658 1654 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.05 % Favored : 89.63 % Rotamer: Outliers : 0.24 % Allowed : 1.68 % Favored : 98.08 % 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 aren not related in a simple way. whole: -1.41 (0.27), residues: 947 helix: 0.30 (0.24), residues: 426 sheet: -1.42 (0.42), residues: 143 loop : -2.16 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 739 TYR 0.012 0.002 TYR A 420 PHE 0.015 0.002 PHE A 976 TRP 0.032 0.003 TRP A 328 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8636) covalent geometry : angle 0.74664 (11897) hydrogen bonds : bond 0.05011 ( 376) hydrogen bonds : angle 4.95075 ( 1040) Misc. bond : bond 0.00261 ( 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 81 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8908 (pmm) cc_final: 0.8611 (pmm) REVERT: A 543 ASP cc_start: 0.9050 (p0) cc_final: 0.8366 (p0) REVERT: A 629 MET cc_start: 0.7618 (pmm) cc_final: 0.7179 (tpt) REVERT: A 756 TRP cc_start: 0.8576 (m100) cc_final: 0.8319 (m100) REVERT: A 807 LEU cc_start: 0.9498 (mt) cc_final: 0.9221 (tt) REVERT: A 887 MET cc_start: 0.8934 (ppp) cc_final: 0.8713 (ppp) REVERT: A 898 PHE cc_start: 0.8752 (m-80) cc_final: 0.8131 (m-80) REVERT: A 922 HIS cc_start: 0.8838 (m90) cc_final: 0.8461 (m-70) REVERT: A 957 MET cc_start: 0.9620 (ttt) cc_final: 0.9209 (tmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0847 time to fit residues: 10.0317 Evaluate side-chains 60 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.062826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.041472 restraints weight = 180828.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.043479 restraints weight = 95792.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.044799 restraints weight = 64519.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045711 restraints weight = 49264.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.046426 restraints weight = 40675.105| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 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 = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2765 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 : 0.695 10.916 11897 Z= 0.335 Chirality : 0.043 0.308 1395 Planarity : 0.004 0.036 1381 Dihedral : 15.262 92.472 1654 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.10 % Favored : 90.48 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % 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 aren not related in a simple way. whole: -1.29 (0.28), residues: 947 helix: 0.38 (0.24), residues: 426 sheet: -1.39 (0.41), residues: 143 loop : -2.05 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.013 0.001 TYR A 420 PHE 0.011 0.001 PHE A1045 TRP 0.017 0.002 TRP A 328 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8636) covalent geometry : angle 0.69517 (11897) hydrogen bonds : bond 0.04092 ( 376) hydrogen bonds : angle 4.68620 ( 1040) Misc. bond : bond 0.00283 ( 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 83 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.7612 (mm110) cc_final: 0.7274 (mm-40) REVERT: A 543 ASP cc_start: 0.9095 (p0) cc_final: 0.8426 (p0) REVERT: A 629 MET cc_start: 0.7578 (pmm) cc_final: 0.7301 (tpt) REVERT: A 756 TRP cc_start: 0.8454 (m100) cc_final: 0.8062 (m100) REVERT: A 807 LEU cc_start: 0.9475 (mt) cc_final: 0.9192 (tt) REVERT: A 887 MET cc_start: 0.8812 (ppp) cc_final: 0.8609 (ppp) REVERT: A 922 HIS cc_start: 0.8901 (m90) cc_final: 0.8538 (m-70) REVERT: A 957 MET cc_start: 0.9586 (ttt) cc_final: 0.9228 (tmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0836 time to fit residues: 10.1836 Evaluate side-chains 65 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 10.0000 chunk 65 optimal weight: 0.0040 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 10.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3630 r_free = 0.3630 target = 0.059382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.038200 restraints weight = 205919.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.040116 restraints weight = 107308.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.041408 restraints weight = 71540.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.042346 restraints weight = 54817.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.043007 restraints weight = 45054.469| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8637 Z= 0.209 Angle : 0.742 9.855 11897 Z= 0.367 Chirality : 0.045 0.312 1395 Planarity : 0.005 0.040 1381 Dihedral : 15.442 91.122 1654 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.95 % Favored : 89.63 % Rotamer: Outliers : 0.24 % Allowed : 1.68 % Favored : 98.08 % 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 aren not related in a simple way. whole: -1.54 (0.27), residues: 947 helix: 0.13 (0.24), residues: 430 sheet: -1.38 (0.42), residues: 140 loop : -2.20 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 492 TYR 0.012 0.002 TYR A 752 PHE 0.017 0.002 PHE A 518 TRP 0.019 0.002 TRP A 961 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8636) covalent geometry : angle 0.74188 (11897) hydrogen bonds : bond 0.05165 ( 376) hydrogen bonds : angle 5.06395 ( 1040) Misc. bond : bond 0.00247 ( 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 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: 0.9141 (p0) cc_final: 0.8792 (p0) REVERT: A 629 MET cc_start: 0.7517 (pmm) cc_final: 0.7268 (tpt) REVERT: A 807 LEU cc_start: 0.9503 (mt) cc_final: 0.9264 (tt) REVERT: A 887 MET cc_start: 0.9066 (ppp) cc_final: 0.8839 (ppp) REVERT: A 922 HIS cc_start: 0.8904 (m90) cc_final: 0.8500 (m-70) REVERT: A 957 MET cc_start: 0.9586 (ttt) cc_final: 0.9111 (tmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0746 time to fit residues: 8.3090 Evaluate side-chains 58 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3716 r_free = 0.3716 target = 0.061967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.040993 restraints weight = 187248.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.042989 restraints weight = 95944.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.044367 restraints weight = 63172.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.045338 restraints weight = 47697.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.046043 restraints weight = 38959.668| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 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 = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3266 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= 0.129 Angle : 0.710 12.515 11897 Z= 0.342 Chirality : 0.044 0.304 1395 Planarity : 0.004 0.041 1381 Dihedral : 15.280 92.360 1654 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.68 % Favored : 90.79 % Rotamer: Outliers : 0.24 % Allowed : 0.72 % Favored : 99.04 % 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 aren not related in a simple way. whole: -1.25 (0.27), residues: 947 helix: 0.29 (0.24), residues: 425 sheet: -1.12 (0.44), residues: 126 loop : -1.96 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.017 0.001 TYR A 437 PHE 0.025 0.001 PHE A 240 TRP 0.050 0.003 TRP A 165 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8636) covalent geometry : angle 0.70981 (11897) hydrogen bonds : bond 0.04033 ( 376) hydrogen bonds : angle 4.73379 ( 1040) Misc. bond : bond 0.00271 ( 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 80 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9082 (p0) cc_final: 0.8434 (p0) REVERT: A 807 LEU cc_start: 0.9492 (mt) cc_final: 0.9220 (tt) REVERT: A 887 MET cc_start: 0.8854 (ppp) cc_final: 0.8589 (ppp) REVERT: A 898 PHE cc_start: 0.8568 (m-80) cc_final: 0.8229 (m-80) REVERT: A 922 HIS cc_start: 0.8896 (m90) cc_final: 0.8514 (m-70) REVERT: A 957 MET cc_start: 0.9510 (ttt) cc_final: 0.9249 (tmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0849 time to fit residues: 9.8695 Evaluate side-chains 65 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3676 r_free = 0.3676 target = 0.060936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039836 restraints weight = 190307.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.041675 restraints weight = 99365.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.043069 restraints weight = 66920.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.044044 restraints weight = 50939.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044744 restraints weight = 41729.674| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3415 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= 0.137 Angle : 0.682 10.112 11897 Z= 0.330 Chirality : 0.043 0.370 1395 Planarity : 0.004 0.037 1381 Dihedral : 15.151 91.297 1654 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.21 % Favored : 90.48 % Rotamer: Outliers : 0.24 % Allowed : 0.96 % Favored : 98.80 % 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 aren not related in a simple way. whole: -1.27 (0.28), residues: 947 helix: 0.39 (0.25), residues: 426 sheet: -1.45 (0.41), residues: 143 loop : -2.01 (0.34), residues: 378 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 0.012 0.001 PHE A 786 TRP 0.026 0.002 TRP A 165 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8636) covalent geometry : angle 0.68214 (11897) hydrogen bonds : bond 0.04111 ( 376) hydrogen bonds : angle 4.71318 ( 1040) Misc. bond : bond 0.00252 ( 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 : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9148 (p0) cc_final: 0.8453 (p0) REVERT: A 807 LEU cc_start: 0.9498 (mt) cc_final: 0.9231 (tt) REVERT: A 887 MET cc_start: 0.8960 (ppp) cc_final: 0.8705 (ppp) REVERT: A 898 PHE cc_start: 0.8611 (m-80) cc_final: 0.8249 (m-80) REVERT: A 922 HIS cc_start: 0.8918 (m90) cc_final: 0.8508 (m-70) REVERT: A 957 MET cc_start: 0.9521 (ttt) cc_final: 0.9247 (tmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0798 time to fit residues: 9.1259 Evaluate side-chains 63 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 0.0470 chunk 75 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.062486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.041296 restraints weight = 169899.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.043210 restraints weight = 94318.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044528 restraints weight = 64927.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.045466 restraints weight = 50321.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.046080 restraints weight = 41680.314| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3571 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= 0.122 Angle : 0.701 11.728 11897 Z= 0.339 Chirality : 0.044 0.355 1395 Planarity : 0.004 0.039 1381 Dihedral : 14.939 91.075 1654 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.57 % Favored : 91.11 % 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 aren not related in a simple way. whole: -1.23 (0.27), residues: 947 helix: 0.37 (0.24), residues: 426 sheet: -1.29 (0.42), residues: 141 loop : -1.97 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.010 0.001 TYR A 437 PHE 0.008 0.001 PHE A 786 TRP 0.026 0.002 TRP A 756 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8636) covalent geometry : angle 0.70130 (11897) hydrogen bonds : bond 0.03762 ( 376) hydrogen bonds : angle 4.69039 ( 1040) Misc. bond : bond 0.00263 ( 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 79 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.307 Fit side-chains REVERT: A 543 ASP cc_start: 0.9128 (p0) cc_final: 0.8448 (p0) REVERT: A 807 LEU cc_start: 0.9495 (mt) cc_final: 0.9227 (tt) REVERT: A 887 MET cc_start: 0.8880 (ppp) cc_final: 0.8652 (ppp) REVERT: A 898 PHE cc_start: 0.8596 (m-80) cc_final: 0.8220 (m-80) REVERT: A 922 HIS cc_start: 0.8998 (m90) cc_final: 0.8600 (m-70) REVERT: A 957 MET cc_start: 0.9554 (ttt) cc_final: 0.9156 (tmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0788 time to fit residues: 9.3620 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 : 0.325 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 958 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.061005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.039608 restraints weight = 216386.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.041570 restraints weight = 109965.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.042982 restraints weight = 72845.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.043930 restraints weight = 54965.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.044672 restraints weight = 45072.302| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3718 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= 0.146 Angle : 0.707 12.453 11897 Z= 0.346 Chirality : 0.044 0.367 1395 Planarity : 0.004 0.036 1381 Dihedral : 14.951 90.381 1654 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.36 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 : 0.11 % 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 aren not related in a simple way. whole: -1.13 (0.28), residues: 947 helix: 0.47 (0.25), residues: 428 sheet: -1.54 (0.44), residues: 117 loop : -1.83 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.009 0.001 TYR A 177 PHE 0.011 0.001 PHE A 240 TRP 0.076 0.004 TRP A 165 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8636) covalent geometry : angle 0.70670 (11897) hydrogen bonds : bond 0.04039 ( 376) hydrogen bonds : angle 4.82031 ( 1040) Misc. bond : bond 0.00238 ( 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 : 0.243 Fit side-chains revert: symmetry clash REVERT: A 538 MET cc_start: -0.5166 (ttm) cc_final: -0.5472 (mmm) REVERT: A 543 ASP cc_start: 0.9188 (p0) cc_final: 0.8513 (p0) REVERT: A 807 LEU cc_start: 0.9503 (mt) cc_final: 0.9241 (tt) REVERT: A 887 MET cc_start: 0.8993 (ppp) cc_final: 0.8746 (ppp) REVERT: A 898 PHE cc_start: 0.8649 (m-80) cc_final: 0.8266 (m-80) REVERT: A 922 HIS cc_start: 0.8979 (m90) cc_final: 0.8582 (m-70) REVERT: A 957 MET cc_start: 0.9539 (ttt) cc_final: 0.9187 (tmm) REVERT: A 1063 CYS cc_start: 0.7415 (p) cc_final: 0.6672 (m) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0718 time to fit residues: 8.0836 Evaluate side-chains 63 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.0770 chunk 78 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.058363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.038241 restraints weight = 181161.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.039986 restraints weight = 99118.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.041206 restraints weight = 68312.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.042090 restraints weight = 52631.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.042713 restraints weight = 43458.639| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8637 Z= 0.210 Angle : 0.776 12.657 11897 Z= 0.386 Chirality : 0.045 0.378 1395 Planarity : 0.005 0.040 1381 Dihedral : 15.317 94.228 1654 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.16 % Favored : 89.52 % 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 aren not related in a simple way. whole: -1.30 (0.27), residues: 947 helix: 0.24 (0.24), residues: 428 sheet: -0.98 (0.45), residues: 130 loop : -2.07 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 739 TYR 0.013 0.001 TYR A1009 PHE 0.015 0.002 PHE A 240 TRP 0.030 0.003 TRP A 961 HIS 0.007 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8636) covalent geometry : angle 0.77621 (11897) hydrogen bonds : bond 0.05004 ( 376) hydrogen bonds : angle 5.12724 ( 1040) Misc. bond : bond 0.00297 ( 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 73 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASP cc_start: 0.9187 (p0) cc_final: 0.8828 (p0) REVERT: A 807 LEU cc_start: 0.9551 (mt) cc_final: 0.9328 (tt) REVERT: A 887 MET cc_start: 0.9069 (ppp) cc_final: 0.8736 (ppp) REVERT: A 957 MET cc_start: 0.9451 (ttt) cc_final: 0.9078 (tmm) REVERT: A 1003 LEU cc_start: 0.9171 (mt) cc_final: 0.8929 (mt) REVERT: A 1047 TYR cc_start: 0.8310 (m-80) cc_final: 0.7701 (m-80) REVERT: A 1063 CYS cc_start: 0.7236 (p) cc_final: 0.6650 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0865 time to fit residues: 9.0706 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 : 0.248 ------------------------------------------------------------------------------- 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: 0.0570 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.0050 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 0.0040 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.0370 chunk 56 optimal weight: 8.9990 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.061752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.041234 restraints weight = 143938.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.043011 restraints weight = 84624.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.044251 restraints weight = 60025.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.045119 restraints weight = 46777.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.045800 restraints weight = 39034.931| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 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 = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8637 Z= 0.136 Angle : 0.749 13.098 11897 Z= 0.362 Chirality : 0.044 0.358 1395 Planarity : 0.004 0.037 1381 Dihedral : 15.099 92.012 1654 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.57 % Favored : 91.01 % 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 aren not related in a simple way. whole: -1.30 (0.27), residues: 947 helix: 0.29 (0.24), residues: 426 sheet: -1.63 (0.45), residues: 117 loop : -1.85 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 237 TYR 0.027 0.001 TYR A 890 PHE 0.012 0.001 PHE A 786 TRP 0.047 0.003 TRP A 165 HIS 0.008 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8636) covalent geometry : angle 0.74904 (11897) hydrogen bonds : bond 0.04011 ( 376) hydrogen bonds : angle 4.81853 ( 1040) Misc. bond : bond 0.00283 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2340.80 seconds wall clock time: 40 minutes 47.70 seconds (2447.70 seconds total)