Starting phenix.real_space_refine on Sat Mar 16 03:35:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9l_15935/03_2024/8b9l_15935.pdb" } resolution = 3.45 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6819 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4335 2.51 5 N 1179 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A GLU 597": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6826 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6948 Time building chain proxies: 6.97, per 1000 atoms: 1.02 Number of scatterers: 6826 At special positions: 0 Unit cell: (72.336, 92.886, 101.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1266 8.00 N 1179 7.00 C 4335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 2.5 seconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 53.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.894A pdb=" N LEU A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.156A pdb=" N THR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.509A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.782A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.902A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.242A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.873A pdb=" N PHE A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.527A pdb=" N ILE A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 598 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.673A pdb=" N PHE A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.682A pdb=" N GLU A 721 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 722 " --> pdb=" O ILE A 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 718 through 722' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.672A pdb=" N ALA A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.054A pdb=" N THR A 800 " --> pdb=" O MET A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.517A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 843 removed outlier: 3.801A pdb=" N MET A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.762A pdb=" N LYS A 912 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.633A pdb=" N CYS A 919 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 953 through 974 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.888A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 4.035A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1101 through 1125 removed outlier: 3.788A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 472 through 473 removed outlier: 3.786A pdb=" N GLU A 472 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 568 removed outlier: 6.857A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 737 through 738 Processing sheet with id=AA4, first strand: chain 'A' and resid 1062 through 1063 removed outlier: 7.939A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1016 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1022 " --> pdb=" O VAL A1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1014 " --> pdb=" O LEU A1022 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 846 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: 2.25 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1151 1.31 - 1.44: 1706 1.44 - 1.56: 4029 1.56 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 6956 Sorted by residual: bond pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.38e-02 5.25e+03 5.94e+01 bond pdb=" C PRO A 565 " pdb=" O PRO A 565 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.14e-02 7.69e+03 1.67e+01 bond pdb=" C PRO A 774 " pdb=" O PRO A 774 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" N ARG A 773 " pdb=" CA ARG A 773 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" N ARG A 771 " pdb=" CA ARG A 771 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.22e-02 6.72e+03 9.75e+00 ... (remaining 6951 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.42: 150 105.42 - 112.81: 3758 112.81 - 120.19: 2580 120.19 - 127.58: 2871 127.58 - 134.97: 65 Bond angle restraints: 9424 Sorted by residual: angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 119.59 134.97 -15.38 1.18e+00 7.18e-01 1.70e+02 angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 118.11 109.66 8.45 1.27e+00 6.20e-01 4.43e+01 angle pdb=" O ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 122.25 115.11 7.14 1.19e+00 7.06e-01 3.60e+01 angle pdb=" O GLY A 770 " pdb=" C GLY A 770 " pdb=" N ARG A 771 " ideal model delta sigma weight residual 122.41 116.89 5.52 1.08e+00 8.57e-01 2.61e+01 angle pdb=" C LEU A 855 " pdb=" CA LEU A 855 " pdb=" CB LEU A 855 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 ... (remaining 9419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3651 17.94 - 35.88: 477 35.88 - 53.82: 118 53.82 - 71.76: 22 71.76 - 89.69: 12 Dihedral angle restraints: 4280 sinusoidal: 1752 harmonic: 2528 Sorted by residual: dihedral pdb=" CD ARG A 771 " pdb=" NE ARG A 771 " pdb=" CZ ARG A 771 " pdb=" NH1 ARG A 771 " ideal model delta sinusoidal sigma weight residual 0.00 85.34 -85.34 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ASN A1097 " pdb=" C ASN A1097 " pdb=" N PHE A1098 " pdb=" CA PHE A1098 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -110.42 -11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 4277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 984 0.085 - 0.170: 94 0.170 - 0.256: 5 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA VAL A 559 " pdb=" N VAL A 559 " pdb=" C VAL A 559 " pdb=" CB VAL A 559 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1081 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 771 " -1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG A 771 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 771 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 771 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 771 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " -0.050 2.00e-02 2.50e+03 9.86e-02 9.72e+01 pdb=" C GLY A 770 " 0.171 2.00e-02 2.50e+03 pdb=" O GLY A 770 " -0.064 2.00e-02 2.50e+03 pdb=" N ARG A 771 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 558 " 0.027 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C GLU A 558 " -0.098 2.00e-02 2.50e+03 pdb=" O GLU A 558 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL A 559 " 0.033 2.00e-02 2.50e+03 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 189 2.70 - 3.25: 7112 3.25 - 3.80: 10872 3.80 - 4.35: 13543 4.35 - 4.90: 22800 Nonbonded interactions: 54516 Sorted by model distance: nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.155 2.440 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.209 2.440 nonbonded pdb=" O ILE A 444 " pdb=" OG SER A 448 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP A 366 " pdb=" ND2 ASN A 370 " model vdw 2.254 2.520 nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.259 2.440 ... (remaining 54511 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 3.760 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.110 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6956 Z= 0.226 Angle : 0.782 15.379 9424 Z= 0.445 Chirality : 0.050 0.426 1084 Planarity : 0.016 0.496 1217 Dihedral : 17.516 89.694 2632 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.41 % Favored : 90.77 % Rotamer: Outliers : 1.18 % Allowed : 22.05 % Favored : 76.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.21 (0.30), residues: 857 helix: 1.38 (0.27), residues: 394 sheet: -0.54 (0.60), residues: 80 loop : -1.74 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 756 HIS 0.003 0.001 HIS A 691 PHE 0.042 0.002 PHE A 672 TYR 0.014 0.001 TYR A 611 ARG 0.007 0.000 ARG A 771 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 170 average time/residue: 0.2167 time to fit residues: 47.8648 Evaluate side-chains 104 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6956 Z= 0.361 Angle : 0.822 9.262 9424 Z= 0.418 Chirality : 0.049 0.221 1084 Planarity : 0.006 0.074 1217 Dihedral : 4.971 32.352 936 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.64 % Favored : 90.42 % Rotamer: Outliers : 3.67 % Allowed : 26.38 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.18 (0.30), residues: 857 helix: 1.35 (0.26), residues: 404 sheet: -0.42 (0.65), residues: 77 loop : -1.76 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1095 HIS 0.005 0.001 HIS A 922 PHE 0.013 0.002 PHE A 570 TYR 0.019 0.002 TYR A1009 ARG 0.012 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.1987 time to fit residues: 31.9636 Evaluate side-chains 107 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6956 Z= 0.232 Angle : 0.800 9.764 9424 Z= 0.396 Chirality : 0.048 0.186 1084 Planarity : 0.006 0.072 1217 Dihedral : 4.844 28.359 934 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.29 % Favored : 90.89 % Rotamer: Outliers : 3.81 % Allowed : 25.98 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.27 (0.30), residues: 857 helix: 1.22 (0.26), residues: 396 sheet: -0.64 (0.65), residues: 71 loop : -1.61 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 932 HIS 0.003 0.001 HIS A 746 PHE 0.017 0.001 PHE A 743 TYR 0.014 0.001 TYR A1009 ARG 0.012 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.6208 (ppp) cc_final: 0.5963 (ppp) outliers start: 27 outliers final: 17 residues processed: 123 average time/residue: 0.1710 time to fit residues: 29.0263 Evaluate side-chains 108 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.215 Angle : 0.778 13.234 9424 Z= 0.383 Chirality : 0.047 0.183 1084 Planarity : 0.006 0.067 1217 Dihedral : 4.812 29.458 934 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.29 % Favored : 90.77 % Rotamer: Outliers : 4.07 % Allowed : 25.07 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.40 (0.30), residues: 857 helix: 1.08 (0.26), residues: 402 sheet: -0.63 (0.68), residues: 66 loop : -1.68 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 PHE 0.016 0.001 PHE A 743 TYR 0.010 0.001 TYR A1009 ARG 0.008 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 121 average time/residue: 0.1753 time to fit residues: 29.3838 Evaluate side-chains 112 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6956 Z= 0.208 Angle : 0.790 13.192 9424 Z= 0.386 Chirality : 0.047 0.187 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.815 28.742 934 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.53 % Favored : 90.65 % Rotamer: Outliers : 4.72 % Allowed : 25.46 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.43 (0.30), residues: 857 helix: 1.05 (0.26), residues: 402 sheet: -0.82 (0.66), residues: 72 loop : -1.67 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 PHE 0.016 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.008 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 30 residues processed: 115 average time/residue: 0.1703 time to fit residues: 27.6352 Evaluate side-chains 117 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0010 chunk 74 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.0000 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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: 0.6139 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6956 Z= 0.207 Angle : 0.806 14.070 9424 Z= 0.392 Chirality : 0.048 0.273 1084 Planarity : 0.005 0.065 1217 Dihedral : 4.698 28.230 934 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.18 % Favored : 91.00 % Rotamer: Outliers : 3.94 % Allowed : 25.59 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.46 (0.30), residues: 857 helix: 0.99 (0.26), residues: 402 sheet: -0.95 (0.64), residues: 77 loop : -1.61 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 932 HIS 0.003 0.001 HIS A 803 PHE 0.017 0.001 PHE A 743 TYR 0.014 0.001 TYR A 479 ARG 0.010 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 26 residues processed: 119 average time/residue: 0.1459 time to fit residues: 24.9561 Evaluate side-chains 115 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6956 Z= 0.281 Angle : 0.801 13.085 9424 Z= 0.396 Chirality : 0.048 0.217 1084 Planarity : 0.005 0.065 1217 Dihedral : 4.741 27.703 934 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.23 % Favored : 90.07 % Rotamer: Outliers : 4.59 % Allowed : 26.77 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.42 (0.30), residues: 857 helix: 1.07 (0.26), residues: 402 sheet: -1.03 (0.66), residues: 71 loop : -1.63 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1095 HIS 0.006 0.001 HIS A 503 PHE 0.017 0.002 PHE A 484 TYR 0.016 0.001 TYR A 479 ARG 0.006 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 29 residues processed: 105 average time/residue: 0.1513 time to fit residues: 23.4117 Evaluate side-chains 108 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 79 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.6181 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6956 Z= 0.206 Angle : 0.807 14.632 9424 Z= 0.389 Chirality : 0.047 0.197 1084 Planarity : 0.005 0.068 1217 Dihedral : 4.699 27.827 934 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.41 % Favored : 90.89 % Rotamer: Outliers : 4.46 % Allowed : 27.43 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.38 (0.30), residues: 857 helix: 1.08 (0.26), residues: 400 sheet: -1.05 (0.66), residues: 71 loop : -1.55 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1095 HIS 0.003 0.001 HIS A 503 PHE 0.016 0.001 PHE A 743 TYR 0.016 0.001 TYR A 479 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 27 residues processed: 112 average time/residue: 0.1387 time to fit residues: 22.6288 Evaluate side-chains 111 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1095 TRP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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: 0.6191 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6956 Z= 0.214 Angle : 0.813 14.627 9424 Z= 0.393 Chirality : 0.047 0.195 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.657 27.186 934 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.23 % Favored : 90.07 % Rotamer: Outliers : 4.72 % Allowed : 27.03 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.38 (0.30), residues: 857 helix: 1.12 (0.26), residues: 400 sheet: -1.10 (0.66), residues: 71 loop : -1.59 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1095 HIS 0.004 0.001 HIS A 503 PHE 0.016 0.001 PHE A 743 TYR 0.018 0.001 TYR A 479 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.6219 (tmm) cc_final: 0.5676 (tmm) outliers start: 34 outliers final: 30 residues processed: 111 average time/residue: 0.1363 time to fit residues: 22.6647 Evaluate side-chains 112 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.0470 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6956 Z= 0.208 Angle : 0.838 15.141 9424 Z= 0.407 Chirality : 0.048 0.202 1084 Planarity : 0.005 0.067 1217 Dihedral : 4.635 26.797 934 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.41 % Favored : 90.89 % Rotamer: Outliers : 4.20 % Allowed : 27.17 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.42 (0.30), residues: 857 helix: 1.06 (0.26), residues: 400 sheet: -1.09 (0.66), residues: 71 loop : -1.58 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1095 HIS 0.004 0.001 HIS A 503 PHE 0.022 0.001 PHE A 667 TYR 0.018 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 28 residues processed: 108 average time/residue: 0.1400 time to fit residues: 22.3878 Evaluate side-chains 112 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.086002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065349 restraints weight = 50600.847| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 10.25 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6956 Z= 0.204 Angle : 0.854 14.886 9424 Z= 0.411 Chirality : 0.048 0.200 1084 Planarity : 0.005 0.068 1217 Dihedral : 4.591 26.515 934 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.76 % Favored : 90.54 % Rotamer: Outliers : 4.33 % Allowed : 27.03 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.39 (0.30), residues: 857 helix: 1.07 (0.26), residues: 400 sheet: -1.08 (0.65), residues: 77 loop : -1.54 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1095 HIS 0.004 0.001 HIS A 503 PHE 0.019 0.001 PHE A 743 TYR 0.018 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.62 seconds wall clock time: 32 minutes 36.27 seconds (1956.27 seconds total)