Starting phenix.real_space_refine on Tue Sep 24 03:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/09_2024/7yam_33717.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4254 2.51 5 N 1116 2.21 5 O 1245 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6672 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6667 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 34, 'TRANS': 836} Chain breaks: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.38, per 1000 atoms: 0.66 Number of scatterers: 6672 At special positions: 0 Unit cell: (80.5359, 86.3718, 130.725, 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 52 16.00 Mg 1 11.99 F 3 9.00 O 1245 8.00 N 1116 7.00 C 4254 6.00 Be 1 4.00 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.800A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 removed outlier: 3.991A pdb=" N SER A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.329A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.618A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 341' Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.840A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.024A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.602A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.648A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 740 Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.537A pdb=" N ALA A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 removed outlier: 3.623A pdb=" N ILE A 759 " --> pdb=" O ASP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.134A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 142 removed outlier: 4.489A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS A 227 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA A 178 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 4.850A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 removed outlier: 5.942A pdb=" N GLY A 658 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 677 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY A 643 " --> pdb=" O MET A 661 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.376A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.376A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.762A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417 413 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.25 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: 2147 1.34 - 1.46: 779 1.46 - 1.58: 3765 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 6775 Sorted by residual: bond pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F3 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N GLN A 747 " pdb=" CA GLN A 747 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.31e-02 5.83e+03 9.51e+00 bond pdb=" F1 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.538 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" CB PRO A 531 " pdb=" CG PRO A 531 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.52e+00 ... (remaining 6770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9117 2.75 - 5.51: 44 5.51 - 8.26: 5 8.26 - 11.02: 1 11.02 - 13.77: 1 Bond angle restraints: 9168 Sorted by residual: angle pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.19 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" F1 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 120.12 109.70 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C ASN A 738 " pdb=" N ILE A 739 " pdb=" CA ILE A 739 " ideal model delta sigma weight residual 122.97 119.83 3.14 9.80e-01 1.04e+00 1.03e+01 angle pdb=" C ASN A 701 " pdb=" N PHE A 702 " pdb=" CA PHE A 702 " ideal model delta sigma weight residual 121.14 116.52 4.62 1.75e+00 3.27e-01 6.96e+00 angle pdb=" N GLN A 747 " pdb=" CA GLN A 747 " pdb=" CB GLN A 747 " ideal model delta sigma weight residual 110.41 114.70 -4.29 1.68e+00 3.54e-01 6.53e+00 ... (remaining 9163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3661 16.82 - 33.65: 374 33.65 - 50.47: 77 50.47 - 67.29: 11 67.29 - 84.11: 11 Dihedral angle restraints: 4134 sinusoidal: 1629 harmonic: 2505 Sorted by residual: dihedral pdb=" CA CYS A 225 " pdb=" C CYS A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta harmonic sigma weight residual 180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB MET A 661 " pdb=" CG MET A 661 " pdb=" SD MET A 661 " pdb=" CE MET A 661 " ideal model delta sinusoidal sigma weight residual 180.00 121.25 58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 735 0.033 - 0.066: 264 0.066 - 0.099: 69 0.099 - 0.132: 33 0.132 - 0.165: 2 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA PHE A 702 " pdb=" N PHE A 702 " pdb=" C PHE A 702 " pdb=" CB PHE A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE A 657 " pdb=" N ILE A 657 " pdb=" C ILE A 657 " pdb=" CB ILE A 657 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA PRO A 531 " pdb=" N PRO A 531 " pdb=" C PRO A 531 " pdb=" CB PRO A 531 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1100 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 747 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C GLN A 747 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN A 747 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 748 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 137 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO A 744 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.021 5.00e-02 4.00e+02 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3717 3.01 - 3.64: 10147 3.64 - 4.27: 14803 4.27 - 4.90: 25787 Nonbonded interactions: 54464 Sorted by model distance: nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.756 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 1.997 2.170 nonbonded pdb=" O ASP A 350 " pdb=" OG1 THR A 354 " model vdw 2.106 3.040 nonbonded pdb=" O THR A 352 " pdb="MG MG A1002 " model vdw 2.132 2.170 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.200 2.170 ... (remaining 54459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.040 Find NCS groups from input model: 0.080 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.003 0.085 6775 Z= 0.233 Angle : 0.535 13.773 9168 Z= 0.272 Chirality : 0.040 0.165 1103 Planarity : 0.004 0.039 1155 Dihedral : 14.474 84.113 2512 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 863 helix: 2.36 (0.24), residues: 478 sheet: -0.15 (0.55), residues: 87 loop : 0.05 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 PHE 0.024 0.002 PHE A 702 TYR 0.006 0.001 TYR A 380 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.765 Fit side-chains REVERT: A 25 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7007 (mttm) REVERT: A 28 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6677 (mp0) REVERT: A 54 ARG cc_start: 0.7331 (mtt90) cc_final: 0.7106 (mtt90) REVERT: A 464 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7536 (mtmm) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1966 time to fit residues: 33.2928 Evaluate side-chains 104 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.207 Angle : 0.499 6.482 9168 Z= 0.265 Chirality : 0.040 0.159 1103 Planarity : 0.004 0.042 1155 Dihedral : 4.387 56.627 919 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.94 % Allowed : 8.16 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.29), residues: 863 helix: 2.42 (0.24), residues: 479 sheet: -0.02 (0.52), residues: 97 loop : 0.12 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 149 PHE 0.023 0.001 PHE A 702 TYR 0.021 0.001 TYR A 75 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.775 Fit side-chains REVERT: A 17 MET cc_start: 0.7770 (tpp) cc_final: 0.7497 (tpt) REVERT: A 25 LYS cc_start: 0.7878 (mmmt) cc_final: 0.6804 (mttm) REVERT: A 54 ARG cc_start: 0.7189 (mtt90) cc_final: 0.6902 (mtt90) REVERT: A 464 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7988 (mtmm) REVERT: A 828 SER cc_start: 0.8582 (t) cc_final: 0.8281 (m) outliers start: 7 outliers final: 7 residues processed: 108 average time/residue: 0.2131 time to fit residues: 30.2177 Evaluate side-chains 104 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6775 Z= 0.217 Angle : 0.494 6.500 9168 Z= 0.260 Chirality : 0.040 0.159 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.860 20.393 916 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.87 % Allowed : 9.89 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 863 helix: 2.39 (0.24), residues: 479 sheet: 0.23 (0.58), residues: 82 loop : 0.15 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.017 0.001 TYR A 75 ARG 0.005 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7687 (mttm) REVERT: A 449 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8150 (mmtm) REVERT: A 464 LYS cc_start: 0.8417 (mtmm) cc_final: 0.7973 (mtmm) REVERT: A 657 ILE cc_start: 0.7251 (mp) cc_final: 0.7015 (mp) REVERT: A 828 SER cc_start: 0.8582 (t) cc_final: 0.8277 (m) REVERT: A 853 MET cc_start: 0.7717 (mmm) cc_final: 0.7466 (mmm) outliers start: 14 outliers final: 10 residues processed: 114 average time/residue: 0.2193 time to fit residues: 32.4735 Evaluate side-chains 107 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6775 Z= 0.205 Angle : 0.489 6.401 9168 Z= 0.257 Chirality : 0.039 0.156 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.835 20.069 916 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 11.50 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 863 helix: 2.42 (0.24), residues: 479 sheet: 0.13 (0.58), residues: 82 loop : 0.12 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.016 0.001 TYR A 75 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7658 (mttm) REVERT: A 449 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8230 (mmtm) REVERT: A 464 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8026 (mttm) REVERT: A 606 GLN cc_start: 0.7377 (tp40) cc_final: 0.7141 (tp40) REVERT: A 828 SER cc_start: 0.8579 (t) cc_final: 0.8291 (m) REVERT: A 853 MET cc_start: 0.7679 (mmm) cc_final: 0.7468 (mmm) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.1932 time to fit residues: 28.3953 Evaluate side-chains 111 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6775 Z= 0.207 Angle : 0.483 6.402 9168 Z= 0.254 Chirality : 0.040 0.156 1103 Planarity : 0.004 0.044 1155 Dihedral : 3.828 20.134 916 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.27 % Allowed : 11.50 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.29), residues: 863 helix: 2.41 (0.24), residues: 480 sheet: -0.29 (0.51), residues: 97 loop : 0.15 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.015 0.001 TYR A 75 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7648 (mttm) REVERT: A 449 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8298 (mmtm) REVERT: A 606 GLN cc_start: 0.7342 (tp40) cc_final: 0.7137 (tp-100) REVERT: A 800 ASP cc_start: 0.6141 (t0) cc_final: 0.5712 (t0) REVERT: A 828 SER cc_start: 0.8575 (t) cc_final: 0.8291 (m) REVERT: A 853 MET cc_start: 0.7684 (mmm) cc_final: 0.7457 (mmm) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 0.1879 time to fit residues: 27.7646 Evaluate side-chains 106 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6775 Z= 0.206 Angle : 0.483 6.493 9168 Z= 0.254 Chirality : 0.040 0.155 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.817 20.077 916 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.01 % Allowed : 12.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.29), residues: 863 helix: 2.45 (0.24), residues: 479 sheet: -0.35 (0.51), residues: 97 loop : 0.19 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7700 (mttm) REVERT: A 449 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8329 (mmtm) REVERT: A 464 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7607 (mtmm) REVERT: A 800 ASP cc_start: 0.6189 (t0) cc_final: 0.5859 (t0) REVERT: A 801 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 828 SER cc_start: 0.8581 (t) cc_final: 0.8293 (m) REVERT: A 853 MET cc_start: 0.7654 (mmm) cc_final: 0.7424 (mmm) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.2046 time to fit residues: 29.1187 Evaluate side-chains 112 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6775 Z= 0.200 Angle : 0.484 6.729 9168 Z= 0.254 Chirality : 0.039 0.157 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.796 20.107 916 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 12.30 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 863 helix: 2.48 (0.24), residues: 478 sheet: 0.00 (0.57), residues: 82 loop : 0.21 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7696 (mttm) REVERT: A 449 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8364 (mmtm) REVERT: A 464 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7755 (mtmm) REVERT: A 800 ASP cc_start: 0.6208 (t0) cc_final: 0.5970 (t0) REVERT: A 801 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 828 SER cc_start: 0.8506 (t) cc_final: 0.8232 (m) REVERT: A 853 MET cc_start: 0.7652 (mmm) cc_final: 0.7424 (mmm) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.2028 time to fit residues: 29.6812 Evaluate side-chains 112 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6775 Z= 0.229 Angle : 0.515 7.373 9168 Z= 0.271 Chirality : 0.040 0.159 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.850 20.220 916 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.81 % Allowed : 13.24 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 863 helix: 2.41 (0.24), residues: 478 sheet: 0.01 (0.57), residues: 82 loop : 0.19 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.001 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.017 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7704 (mttm) REVERT: A 449 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8368 (mmtm) REVERT: A 464 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7523 (mtmm) REVERT: A 800 ASP cc_start: 0.6171 (t0) cc_final: 0.5937 (t0) REVERT: A 801 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7728 (t0) REVERT: A 828 SER cc_start: 0.8592 (t) cc_final: 0.8298 (m) REVERT: A 853 MET cc_start: 0.7692 (mmm) cc_final: 0.7470 (mmm) outliers start: 21 outliers final: 18 residues processed: 109 average time/residue: 0.1861 time to fit residues: 27.2135 Evaluate side-chains 115 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.162 Angle : 0.492 7.238 9168 Z= 0.256 Chirality : 0.039 0.153 1103 Planarity : 0.004 0.047 1155 Dihedral : 3.699 19.256 916 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.60 % Allowed : 14.30 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 863 helix: 2.58 (0.23), residues: 478 sheet: 0.01 (0.57), residues: 82 loop : 0.21 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 140 PHE 0.024 0.001 PHE A 702 TYR 0.010 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7637 (mttm) REVERT: A 449 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8362 (mmtm) REVERT: A 464 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7547 (mtmm) REVERT: A 801 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7589 (t0) REVERT: A 828 SER cc_start: 0.8488 (t) cc_final: 0.8258 (m) REVERT: A 853 MET cc_start: 0.7697 (mmm) cc_final: 0.7471 (mmm) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.2073 time to fit residues: 30.1322 Evaluate side-chains 106 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6775 Z= 0.218 Angle : 0.520 7.165 9168 Z= 0.273 Chirality : 0.040 0.165 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.758 19.595 916 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.74 % Allowed : 14.84 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 863 helix: 2.50 (0.23), residues: 478 sheet: -0.01 (0.58), residues: 82 loop : 0.17 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.000 HIS A 140 PHE 0.023 0.001 PHE A 702 TYR 0.008 0.001 TYR A 380 ARG 0.002 0.000 ARG A 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7636 (mttm) REVERT: A 449 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8368 (mmtm) REVERT: A 464 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7532 (mtmm) REVERT: A 801 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7588 (t0) REVERT: A 828 SER cc_start: 0.8551 (t) cc_final: 0.8300 (m) REVERT: A 853 MET cc_start: 0.7699 (mmm) cc_final: 0.7472 (mmm) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1955 time to fit residues: 26.3886 Evaluate side-chains 103 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127001 restraints weight = 6957.708| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.45 r_work: 0.3396 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6775 Z= 0.240 Angle : 0.528 7.517 9168 Z= 0.276 Chirality : 0.040 0.166 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.841 20.689 916 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 14.57 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 863 helix: 2.42 (0.23), residues: 478 sheet: -0.06 (0.58), residues: 82 loop : 0.21 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.001 HIS A 140 PHE 0.022 0.001 PHE A 702 TYR 0.008 0.001 TYR A 272 ARG 0.002 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.30 seconds wall clock time: 31 minutes 10.74 seconds (1870.74 seconds total)