Starting phenix.real_space_refine on Sat Dec 28 21:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpi_24615/12_2024/7rpi_24615.cif" } resolution = 2.5 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= 0.005 sd= 0.579 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 Na 2 4.78 5 C 5741 2.51 5 N 1184 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8526 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 bond proxies already assigned to first conformer: 7550 Chain: "A" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1163 Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'undetermined': 35, 'water': 43} Link IDs: {None: 77} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.59, per 1000 atoms: 1.12 Number of scatterers: 8526 At special positions: 0 Unit cell: (86.005, 87.675, 127.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Na 2 11.00 O 1534 8.00 N 1184 7.00 C 5741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.04 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2129 " - " ASN A 915 " " NAG A2130 " - " ASN A 834 " " NAG A2131 " - " ASN A 475 " " NAG A2132 " - " ASN A 390 " " NAG A2133 " - " ASN A 362 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.9 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 2 sheets defined 66.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.552A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.827A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.564A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.630A pdb=" N LEU A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 5.239A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 490 through 502 removed outlier: 3.827A pdb=" N GLN A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.653A pdb=" N THR A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 587 removed outlier: 3.642A pdb=" N VAL A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 620 removed outlier: 5.557A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 682 through 706 removed outlier: 4.586A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.720A pdb=" N CYS A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.689A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.608A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 880 through 899 removed outlier: 3.978A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 969 through 1002 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.590A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 5.434A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 4.013A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.577A pdb=" N ALA A 920 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 923 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP A 789 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE A 925 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 787 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER A 927 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 785 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 929 " --> pdb=" O MET A 783 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1287 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: 2.62 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1340 1.32 - 1.45: 2192 1.45 - 1.58: 5065 1.58 - 1.70: 69 1.70 - 1.83: 98 Bond restraints: 8764 Sorted by residual: bond pdb=" N MET A 557 " pdb=" CA BMET A 557 " ideal model delta sigma weight residual 1.458 1.357 0.102 1.27e-02 6.20e+03 6.43e+01 bond pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 1.454 1.400 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" C ASP A 578 " pdb=" O ASP A 578 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" CA GLU A1031 " pdb=" CB GLU A1031 " ideal model delta sigma weight residual 1.535 1.462 0.073 1.93e-02 2.68e+03 1.42e+01 bond pdb=" CB THR A1122 " pdb=" OG1 THR A1122 " ideal model delta sigma weight residual 1.433 1.373 0.060 1.60e-02 3.91e+03 1.42e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 10331 2.65 - 5.31: 1646 5.31 - 7.96: 76 7.96 - 10.61: 8 10.61 - 13.26: 1 Bond angle restraints: 12062 Sorted by residual: angle pdb=" N ARG A 341 " pdb=" CA ARG A 341 " pdb=" C ARG A 341 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.69e+00 3.50e-01 6.16e+01 angle pdb=" N MET A 557 " pdb=" CA BMET A 557 " pdb=" C MET A 557 " ideal model delta sigma weight residual 111.75 120.36 -8.61 1.28e+00 6.10e-01 4.52e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.40 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE A 549 " pdb=" CB PHE A 549 " pdb=" CG PHE A 549 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP A 293 " pdb=" CB ASP A 293 " pdb=" CG ASP A 293 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 12057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 6362 26.89 - 53.79: 229 53.79 - 80.68: 41 80.68 - 107.57: 21 107.57 - 134.47: 6 Dihedral angle restraints: 6659 sinusoidal: 3931 harmonic: 2728 Sorted by residual: dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ASN A 421 " pdb=" CA ASN A 421 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A 443 " pdb=" C TYR A 443 " pdb=" N ALA A 444 " pdb=" CA ALA A 444 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 922 0.095 - 0.191: 432 0.191 - 0.286: 69 0.286 - 0.381: 15 0.381 - 0.477: 3 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA GLU A1031 " pdb=" N GLU A1031 " pdb=" C GLU A1031 " pdb=" CB GLU A1031 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA BMET A 557 " pdb=" N MET A 557 " pdb=" C MET A 557 " pdb=" CB BMET A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 1438 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 834 " -0.102 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A 834 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 834 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 834 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG A2130 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.145 2.00e-02 2.50e+03 7.20e-02 1.30e+02 pdb=" CG TRP A 313 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " -0.091 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" CG ASN A 915 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.164 2.00e-02 2.50e+03 pdb=" C1 NAG A2129 " -0.119 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 140 2.72 - 3.26: 8270 3.26 - 3.81: 12726 3.81 - 4.35: 18480 4.35 - 4.90: 29510 Nonbonded interactions: 69126 Sorted by model distance: nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A2134 " model vdw 2.170 2.470 nonbonded pdb=" O GLY A1045 " pdb="NA NA A2134 " model vdw 2.205 2.470 nonbonded pdb=" OD1 ASP A 572 " pdb="NA NA A2135 " model vdw 2.213 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A2135 " model vdw 2.245 2.470 nonbonded pdb="NA NA A2135 " pdb=" O HOH A2231 " model vdw 2.261 2.470 ... (remaining 69121 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.060 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:16.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.016 0.102 8764 Z= 0.968 Angle : 1.818 13.262 12062 Z= 1.185 Chirality : 0.106 0.477 1441 Planarity : 0.014 0.100 1339 Dihedral : 14.731 134.467 4869 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 919 helix: -0.43 (0.19), residues: 558 sheet: 0.48 (0.94), residues: 29 loop : -0.29 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.145 0.028 TRP A 313 HIS 0.008 0.003 HIS A 332 PHE 0.063 0.014 PHE A1109 TYR 0.114 0.021 TYR A 635 ARG 0.007 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TRP cc_start: 0.7100 (m-10) cc_final: 0.6769 (m-10) REVERT: A 194 MET cc_start: 0.5966 (mtp) cc_final: 0.5583 (mmp) REVERT: A 647 MET cc_start: 0.7973 (mmp) cc_final: 0.7606 (mmt) REVERT: A 698 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 700 SER cc_start: 0.7653 (t) cc_final: 0.7056 (m) REVERT: A 701 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6546 (tpm170) REVERT: A 702 ILE cc_start: 0.6853 (mm) cc_final: 0.6584 (mm) REVERT: A 860 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (t0) REVERT: A 937 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7445 (mtmm) REVERT: A 943 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6813 (mmmt) REVERT: A 997 MET cc_start: 0.7552 (mtm) cc_final: 0.7263 (mtp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 1.3385 time to fit residues: 183.8019 Evaluate side-chains 87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 340 GLN A 421 ASN A 465 ASN A 470 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8764 Z= 0.187 Angle : 0.698 9.686 12062 Z= 0.334 Chirality : 0.043 0.226 1441 Planarity : 0.004 0.034 1339 Dihedral : 11.630 166.974 3198 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.35 % Allowed : 6.39 % Favored : 92.26 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.50 % 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: 1.60 (0.28), residues: 919 helix: 1.56 (0.21), residues: 568 sheet: 0.71 (0.90), residues: 29 loop : 0.35 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 474 HIS 0.007 0.001 HIS A 827 PHE 0.016 0.002 PHE A 608 TYR 0.015 0.002 TYR A 619 ARG 0.003 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5955 (mtp) cc_final: 0.5536 (mmp) REVERT: A 223 GLU cc_start: 0.7700 (tt0) cc_final: 0.6680 (pm20) REVERT: A 340 GLN cc_start: 0.7121 (tt0) cc_final: 0.6866 (mt0) REVERT: A 363 ARG cc_start: 0.7191 (mpt90) cc_final: 0.6961 (mpt90) REVERT: A 515 LEU cc_start: 0.6752 (mt) cc_final: 0.6426 (tp) REVERT: A 698 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6198 (mm-30) REVERT: A 700 SER cc_start: 0.7496 (t) cc_final: 0.7001 (m) REVERT: A 701 ARG cc_start: 0.6884 (mmt90) cc_final: 0.6384 (tpm170) REVERT: A 746 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6647 (mm-30) REVERT: A 771 MET cc_start: 0.7402 (mpp) cc_final: 0.7134 (mmp) REVERT: A 887 CYS cc_start: 0.6930 (m) cc_final: 0.6468 (m) REVERT: A 962 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6121 (mtm110) REVERT: A 1059 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7244 (ttt-90) outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 1.2465 time to fit residues: 142.6728 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.169 Angle : 0.634 8.038 12062 Z= 0.296 Chirality : 0.042 0.319 1441 Planarity : 0.004 0.042 1339 Dihedral : 11.001 179.858 3198 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.60 % Allowed : 9.09 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.99 (0.28), residues: 919 helix: 1.95 (0.22), residues: 573 sheet: 0.87 (0.94), residues: 29 loop : 0.30 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.004 0.001 HIS A 827 PHE 0.017 0.001 PHE A 608 TYR 0.014 0.002 TYR A 619 ARG 0.006 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5797 (mtp) cc_final: 0.5372 (mmp) REVERT: A 223 GLU cc_start: 0.7669 (tt0) cc_final: 0.6685 (pm20) REVERT: A 339 CYS cc_start: 0.6533 (p) cc_final: 0.5940 (p) REVERT: A 515 LEU cc_start: 0.6633 (mt) cc_final: 0.6354 (tt) REVERT: A 700 SER cc_start: 0.7526 (t) cc_final: 0.7013 (m) REVERT: A 701 ARG cc_start: 0.6851 (mmt90) cc_final: 0.6367 (tpm170) REVERT: A 746 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6576 (mm-30) REVERT: A 771 MET cc_start: 0.7409 (mpp) cc_final: 0.7133 (mmp) REVERT: A 887 CYS cc_start: 0.6925 (m) cc_final: 0.6451 (m) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 1.2696 time to fit residues: 143.8705 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8764 Z= 0.184 Angle : 0.619 7.661 12062 Z= 0.293 Chirality : 0.042 0.383 1441 Planarity : 0.004 0.044 1339 Dihedral : 10.587 175.580 3198 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.09 % Allowed : 9.71 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.04 (0.28), residues: 919 helix: 2.13 (0.22), residues: 567 sheet: 0.86 (0.91), residues: 29 loop : 0.05 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 827 PHE 0.019 0.001 PHE A 608 TYR 0.013 0.002 TYR A 644 ARG 0.004 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5768 (mtp) cc_final: 0.5315 (mmp) REVERT: A 223 GLU cc_start: 0.7648 (tt0) cc_final: 0.6775 (pm20) REVERT: A 363 ARG cc_start: 0.7412 (mpt90) cc_final: 0.7142 (mtt-85) REVERT: A 515 LEU cc_start: 0.6592 (mt) cc_final: 0.6304 (tt) REVERT: A 700 SER cc_start: 0.7485 (t) cc_final: 0.6970 (m) REVERT: A 701 ARG cc_start: 0.6790 (mmt90) cc_final: 0.6308 (tpm170) REVERT: A 746 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6555 (mm-30) REVERT: A 771 MET cc_start: 0.7361 (mpp) cc_final: 0.6857 (mmp) REVERT: A 887 CYS cc_start: 0.6922 (m) cc_final: 0.6448 (m) REVERT: A 937 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6474 (mmpt) REVERT: A 943 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6674 (tptt) outliers start: 17 outliers final: 6 residues processed: 105 average time/residue: 1.2140 time to fit residues: 136.3495 Evaluate side-chains 95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8764 Z= 0.182 Angle : 0.603 7.214 12062 Z= 0.286 Chirality : 0.042 0.354 1441 Planarity : 0.004 0.041 1339 Dihedral : 10.338 167.980 3198 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.28), residues: 919 helix: 2.17 (0.22), residues: 566 sheet: 0.90 (0.92), residues: 29 loop : 0.01 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 PHE 0.018 0.001 PHE A 608 TYR 0.012 0.002 TYR A 644 ARG 0.004 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5783 (mtp) cc_final: 0.5338 (mmp) REVERT: A 223 GLU cc_start: 0.7661 (tt0) cc_final: 0.6836 (pm20) REVERT: A 363 ARG cc_start: 0.7395 (mpt90) cc_final: 0.7073 (mtt-85) REVERT: A 515 LEU cc_start: 0.6579 (mt) cc_final: 0.6314 (tt) REVERT: A 700 SER cc_start: 0.7469 (t) cc_final: 0.6945 (m) REVERT: A 701 ARG cc_start: 0.6710 (mmt90) cc_final: 0.6229 (tpm170) REVERT: A 746 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6490 (pt0) REVERT: A 771 MET cc_start: 0.7329 (mpp) cc_final: 0.6813 (mmp) REVERT: A 887 CYS cc_start: 0.6861 (m) cc_final: 0.6404 (m) REVERT: A 937 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6433 (mmpt) REVERT: A 943 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6675 (tptt) REVERT: A 1096 MET cc_start: 0.7848 (mmm) cc_final: 0.7636 (mmp) outliers start: 15 outliers final: 4 residues processed: 101 average time/residue: 1.2952 time to fit residues: 140.0361 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8764 Z= 0.181 Angle : 0.603 8.205 12062 Z= 0.285 Chirality : 0.041 0.347 1441 Planarity : 0.004 0.042 1339 Dihedral : 10.206 164.930 3198 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.60 % Allowed : 11.55 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.05 (0.28), residues: 919 helix: 2.19 (0.22), residues: 566 sheet: 0.86 (0.90), residues: 29 loop : -0.06 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 PHE 0.017 0.001 PHE A 608 TYR 0.012 0.001 TYR A 644 ARG 0.004 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5783 (mtp) cc_final: 0.5338 (mmp) REVERT: A 223 GLU cc_start: 0.7614 (tt0) cc_final: 0.6768 (pm20) REVERT: A 363 ARG cc_start: 0.7382 (mpt90) cc_final: 0.7085 (mtt-85) REVERT: A 515 LEU cc_start: 0.6592 (mt) cc_final: 0.6321 (tt) REVERT: A 700 SER cc_start: 0.7468 (t) cc_final: 0.6948 (m) REVERT: A 701 ARG cc_start: 0.6720 (mmt90) cc_final: 0.6231 (tpm170) REVERT: A 745 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6704 (pt) REVERT: A 746 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6493 (pt0) REVERT: A 771 MET cc_start: 0.7304 (mpp) cc_final: 0.7080 (mmp) REVERT: A 887 CYS cc_start: 0.6859 (m) cc_final: 0.6422 (m) REVERT: A 937 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6452 (mmpt) REVERT: A 943 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6677 (tptt) REVERT: A 1096 MET cc_start: 0.7871 (mmm) cc_final: 0.7621 (mmp) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 1.1615 time to fit residues: 117.2615 Evaluate side-chains 97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1008 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8764 Z= 0.155 Angle : 0.570 8.831 12062 Z= 0.269 Chirality : 0.040 0.337 1441 Planarity : 0.004 0.043 1339 Dihedral : 9.936 163.068 3198 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.47 % Allowed : 11.67 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.14 (0.29), residues: 919 helix: 2.28 (0.22), residues: 566 sheet: 0.91 (0.92), residues: 29 loop : -0.05 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 PHE 0.013 0.001 PHE A 608 TYR 0.011 0.001 TYR A 545 ARG 0.003 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.871 Fit side-chains REVERT: A 194 MET cc_start: 0.5848 (mtp) cc_final: 0.5452 (mmp) REVERT: A 223 GLU cc_start: 0.7569 (tt0) cc_final: 0.6773 (pm20) REVERT: A 363 ARG cc_start: 0.7384 (mpt90) cc_final: 0.7098 (mtt-85) REVERT: A 515 LEU cc_start: 0.6520 (mt) cc_final: 0.6296 (tt) REVERT: A 700 SER cc_start: 0.7465 (t) cc_final: 0.6955 (m) REVERT: A 701 ARG cc_start: 0.6742 (mmt90) cc_final: 0.6230 (tpm170) REVERT: A 745 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6699 (pt) REVERT: A 746 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6360 (pt0) REVERT: A 771 MET cc_start: 0.7268 (mpp) cc_final: 0.6805 (mmp) REVERT: A 887 CYS cc_start: 0.6863 (m) cc_final: 0.6432 (m) REVERT: A 937 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6384 (mmpt) REVERT: A 943 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6756 (tptt) REVERT: A 1096 MET cc_start: 0.7834 (mmm) cc_final: 0.7603 (mmp) outliers start: 12 outliers final: 3 residues processed: 100 average time/residue: 1.1625 time to fit residues: 125.0146 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1008 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8764 Z= 0.191 Angle : 0.604 9.004 12062 Z= 0.287 Chirality : 0.041 0.330 1441 Planarity : 0.004 0.043 1339 Dihedral : 10.012 162.176 3198 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.35 % Allowed : 12.04 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.00 (0.28), residues: 919 helix: 2.20 (0.22), residues: 568 sheet: 0.89 (0.89), residues: 29 loop : -0.19 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 332 PHE 0.021 0.002 PHE A 585 TYR 0.012 0.002 TYR A 644 ARG 0.005 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.734 Fit side-chains REVERT: A 194 MET cc_start: 0.5745 (mtp) cc_final: 0.5293 (mmp) REVERT: A 223 GLU cc_start: 0.7597 (tt0) cc_final: 0.6794 (pm20) REVERT: A 363 ARG cc_start: 0.7402 (mpt90) cc_final: 0.7107 (mtt-85) REVERT: A 515 LEU cc_start: 0.6560 (mt) cc_final: 0.6291 (tt) REVERT: A 700 SER cc_start: 0.7469 (t) cc_final: 0.6944 (m) REVERT: A 701 ARG cc_start: 0.6687 (mmt90) cc_final: 0.6194 (tpm170) REVERT: A 746 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6511 (pt0) REVERT: A 887 CYS cc_start: 0.6876 (m) cc_final: 0.6408 (m) REVERT: A 937 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6441 (mmpt) REVERT: A 943 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6670 (tptt) REVERT: A 1096 MET cc_start: 0.7860 (mmm) cc_final: 0.7637 (mmp) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 1.0751 time to fit residues: 108.0146 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8764 Z= 0.180 Angle : 0.606 9.164 12062 Z= 0.285 Chirality : 0.041 0.333 1441 Planarity : 0.004 0.044 1339 Dihedral : 9.961 161.205 3198 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.61 % Allowed : 13.02 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.00 (0.28), residues: 919 helix: 2.23 (0.22), residues: 568 sheet: 0.91 (0.90), residues: 29 loop : -0.26 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 602 PHE 0.016 0.001 PHE A 608 TYR 0.012 0.001 TYR A 644 ARG 0.005 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.027 Fit side-chains REVERT: A 194 MET cc_start: 0.5770 (mtp) cc_final: 0.5339 (mmp) REVERT: A 223 GLU cc_start: 0.7585 (tt0) cc_final: 0.6802 (pm20) REVERT: A 363 ARG cc_start: 0.7336 (mpt90) cc_final: 0.7040 (mtt-85) REVERT: A 515 LEU cc_start: 0.6608 (mt) cc_final: 0.6335 (tt) REVERT: A 700 SER cc_start: 0.7466 (t) cc_final: 0.6944 (m) REVERT: A 701 ARG cc_start: 0.6679 (mmt90) cc_final: 0.6181 (tpm170) REVERT: A 746 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6482 (pt0) REVERT: A 887 CYS cc_start: 0.6851 (m) cc_final: 0.6444 (m) REVERT: A 937 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6452 (mmpt) REVERT: A 943 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6747 (tptt) REVERT: A 1096 MET cc_start: 0.7848 (mmm) cc_final: 0.7623 (mmp) outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 1.1150 time to fit residues: 110.4765 Evaluate side-chains 93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 0.0060 chunk 84 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8764 Z= 0.152 Angle : 0.581 10.233 12062 Z= 0.273 Chirality : 0.040 0.332 1441 Planarity : 0.004 0.044 1339 Dihedral : 9.793 160.198 3198 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.61 % Allowed : 13.14 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.13 (0.29), residues: 919 helix: 2.34 (0.22), residues: 566 sheet: 1.05 (0.92), residues: 29 loop : -0.22 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.001 0.000 HIS A 332 PHE 0.011 0.001 PHE A 608 TYR 0.011 0.001 TYR A 545 ARG 0.004 0.000 ARG A 962 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.760 Fit side-chains REVERT: A 194 MET cc_start: 0.5841 (mtp) cc_final: 0.5455 (mmp) REVERT: A 223 GLU cc_start: 0.7572 (tt0) cc_final: 0.6769 (pm20) REVERT: A 363 ARG cc_start: 0.7303 (mpt90) cc_final: 0.7011 (mtt-85) REVERT: A 515 LEU cc_start: 0.6528 (mt) cc_final: 0.6294 (tt) REVERT: A 700 SER cc_start: 0.7437 (t) cc_final: 0.6932 (m) REVERT: A 701 ARG cc_start: 0.6672 (mmt90) cc_final: 0.6175 (tpm170) REVERT: A 746 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6247 (pm20) REVERT: A 887 CYS cc_start: 0.6883 (m) cc_final: 0.6401 (m) REVERT: A 937 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6369 (mmpt) REVERT: A 943 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6756 (tptt) REVERT: A 1096 MET cc_start: 0.7839 (mmm) cc_final: 0.7631 (mmp) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 1.1366 time to fit residues: 114.9925 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140348 restraints weight = 11234.218| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.06 r_work: 0.3526 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8764 Z= 0.163 Angle : 0.589 10.996 12062 Z= 0.277 Chirality : 0.040 0.325 1441 Planarity : 0.004 0.044 1339 Dihedral : 9.778 159.187 3198 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.61 % Allowed : 13.14 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.07 (0.28), residues: 919 helix: 2.29 (0.22), residues: 568 sheet: 1.06 (0.92), residues: 29 loop : -0.27 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.001 0.000 HIS A 602 PHE 0.015 0.001 PHE A 608 TYR 0.011 0.001 TYR A 545 ARG 0.004 0.000 ARG A 962 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.76 seconds wall clock time: 56 minutes 52.66 seconds (3412.66 seconds total)