Starting phenix.real_space_refine on Tue Feb 13 21:24:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7roz_24610/02_2024/7roz_24610.pdb" } resolution = 3.1 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= 0.001 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 Mg 1 5.21 5 S 47 5.16 5 C 4897 2.51 5 N 1343 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 101": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 841": "OD1" <-> "OD2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A ASP 883": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 7774 Unusual residues: {' MG': 1} Classifications: {'peptide': 1064, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 38, 'TRANS': 1025, None: 1} Not linked: pdbres="GLN A1121 " pdbres=" MG A1201 " Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1015 Unresolved non-hydrogen dihedrals: 715 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 15, 'GLU:plan': 20, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 487 Time building chain proxies: 4.57, per 1000 atoms: 0.59 Number of scatterers: 7774 At special positions: 0 Unit cell: (96.216, 102.124, 81.868, 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 47 16.00 Mg 1 11.99 O 1486 8.00 N 1343 7.00 C 4897 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 36.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.858A pdb=" N GLN A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 5.768A pdb=" N SER A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.501A pdb=" N LEU A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.541A pdb=" N ASN A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.608A pdb=" N ILE A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.826A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 645 through 662 removed outlier: 3.840A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.810A pdb=" N ALA A 669 " --> pdb=" O ASP A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.519A pdb=" N GLN A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 720 Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.565A pdb=" N LYS A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 884 through 897 Processing helix chain 'A' and resid 905 through 921 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.867A pdb=" N ARG A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 998 through 1017 removed outlier: 4.113A pdb=" N HIS A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A1008 " --> pdb=" O ASP A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1053 Processing helix chain 'A' and resid 1055 through 1067 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.957A pdb=" N VAL A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1121 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.983A pdb=" N ALA A 57 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 169 removed outlier: 6.964A pdb=" N ARG A 105 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP A 135 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 107 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 133 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE A 109 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 127 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 125 removed outlier: 6.176A pdb=" N PHE A 123 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 400 removed outlier: 5.339A pdb=" N LEU A 393 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 385 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 395 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 383 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 415 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN A 382 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 417 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TRP A 485 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.843A pdb=" N LEU A 618 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 582 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP A 623 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 580 " --> pdb=" O TRP A 623 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 593 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 749 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS A 811 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 734 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.219A pdb=" N PHE A 939 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 339 hydrogen bonds defined for protein. 963 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: 3.13 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2631 1.34 - 1.46: 1298 1.46 - 1.57: 3893 1.57 - 1.69: 1 1.69 - 1.81: 72 Bond restraints: 7895 Sorted by residual: bond pdb=" CB PRO A 940 " pdb=" CG PRO A 940 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.11e+00 bond pdb=" CB GLN A 567 " pdb=" CG GLN A 567 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.79e-01 bond pdb=" C ASN A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.75e-01 bond pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.54e-02 4.22e+03 6.76e-01 bond pdb=" CG LEU A 911 " pdb=" CD2 LEU A 911 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.96e-01 ... (remaining 7890 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.67: 138 105.67 - 112.74: 4278 112.74 - 119.82: 2485 119.82 - 126.90: 3740 126.90 - 133.97: 71 Bond angle restraints: 10712 Sorted by residual: angle pdb=" CA PRO A 940 " pdb=" N PRO A 940 " pdb=" CD PRO A 940 " ideal model delta sigma weight residual 112.00 106.81 5.19 1.40e+00 5.10e-01 1.37e+01 angle pdb=" N LYS A 610 " pdb=" CA LYS A 610 " pdb=" C LYS A 610 " ideal model delta sigma weight residual 114.04 110.14 3.90 1.24e+00 6.50e-01 9.88e+00 angle pdb=" C ASP A 119 " pdb=" N GLU A 120 " pdb=" CA GLU A 120 " ideal model delta sigma weight residual 121.54 127.05 -5.51 1.91e+00 2.74e-01 8.32e+00 angle pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 angle pdb=" C VAL A 956 " pdb=" N PHE A 957 " pdb=" CA PHE A 957 " ideal model delta sigma weight residual 122.61 126.38 -3.77 1.56e+00 4.11e-01 5.85e+00 ... (remaining 10707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4299 15.78 - 31.55: 361 31.55 - 47.33: 103 47.33 - 63.11: 17 63.11 - 78.88: 7 Dihedral angle restraints: 4787 sinusoidal: 1689 harmonic: 3098 Sorted by residual: dihedral pdb=" CA VAL A 66 " pdb=" C VAL A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 851 " pdb=" C PRO A 851 " pdb=" N PRO A 852 " pdb=" CA PRO A 852 " ideal model delta harmonic sigma weight residual 180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA SER A 68 " pdb=" C SER A 68 " pdb=" N ARG A 69 " pdb=" CA ARG A 69 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 843 0.035 - 0.069: 289 0.069 - 0.103: 98 0.103 - 0.138: 33 0.138 - 0.172: 3 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 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 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1263 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 939 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 940 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 940 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 940 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 850 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 851 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 627 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 628 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.035 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 82 2.63 - 3.20: 7370 3.20 - 3.77: 12257 3.77 - 4.33: 16872 4.33 - 4.90: 26779 Nonbonded interactions: 63360 Sorted by model distance: nonbonded pdb=" OD1 ASP A 832 " pdb="MG MG A1201 " model vdw 2.064 2.170 nonbonded pdb=" OD2 ASP A 834 " pdb="MG MG A1201 " model vdw 2.108 2.170 nonbonded pdb=" O LYS A 566 " pdb=" NE2 GLN A 570 " model vdw 2.202 2.520 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.230 2.440 nonbonded pdb=" NH2 ARG A 633 " pdb=" O LYS A 718 " model vdw 2.288 2.520 ... (remaining 63355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.020 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7895 Z= 0.162 Angle : 0.543 6.992 10712 Z= 0.297 Chirality : 0.042 0.172 1266 Planarity : 0.005 0.115 1394 Dihedral : 13.572 78.881 2763 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 1047 helix: 0.52 (0.28), residues: 378 sheet: -2.31 (0.42), residues: 152 loop : -1.78 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.019 0.001 PHE A 251 TYR 0.015 0.001 TYR A 747 ARG 0.008 0.001 ARG A 729 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.924 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: A 155 LYS cc_start: 0.6239 (mtmm) cc_final: 0.5837 (mtmm) REVERT: A 311 PHE cc_start: 0.7238 (t80) cc_final: 0.7036 (t80) REVERT: A 331 LEU cc_start: 0.8136 (mm) cc_final: 0.7929 (mt) REVERT: A 864 ASP cc_start: 0.7488 (p0) cc_final: 0.7227 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2473 time to fit residues: 58.5605 Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 538 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN A 619 ASN A 816 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 7895 Z= 0.456 Angle : 0.724 11.537 10712 Z= 0.374 Chirality : 0.047 0.174 1266 Planarity : 0.005 0.067 1394 Dihedral : 4.985 25.182 1117 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.71 % Allowed : 11.04 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1047 helix: 0.42 (0.26), residues: 389 sheet: -2.29 (0.41), residues: 139 loop : -1.85 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.006 0.002 HIS A 822 PHE 0.019 0.002 PHE A 957 TYR 0.017 0.002 TYR A 799 ARG 0.007 0.001 ARG A 937 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 ASP cc_start: 0.7542 (p0) cc_final: 0.7259 (p0) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.2164 time to fit residues: 28.5304 Evaluate side-chains 80 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 915 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7895 Z= 0.220 Angle : 0.605 11.970 10712 Z= 0.310 Chirality : 0.044 0.261 1266 Planarity : 0.004 0.054 1394 Dihedral : 4.760 23.730 1117 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.37 % Allowed : 12.61 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 1047 helix: 0.52 (0.26), residues: 386 sheet: -2.30 (0.40), residues: 136 loop : -1.79 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.011 0.001 HIS A 865 PHE 0.022 0.002 PHE A 203 TYR 0.014 0.001 TYR A 808 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 ASP cc_start: 0.7498 (p0) cc_final: 0.7237 (p0) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 0.1665 time to fit residues: 22.6587 Evaluate side-chains 82 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7895 Z= 0.334 Angle : 0.617 11.412 10712 Z= 0.323 Chirality : 0.045 0.206 1266 Planarity : 0.004 0.047 1394 Dihedral : 4.842 24.416 1117 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.15 % Allowed : 13.80 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), residues: 1047 helix: 0.58 (0.26), residues: 385 sheet: -2.28 (0.41), residues: 136 loop : -1.76 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.016 0.002 PHE A 181 TYR 0.014 0.001 TYR A 808 ARG 0.004 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 ASP cc_start: 0.7463 (p0) cc_final: 0.7157 (p0) outliers start: 24 outliers final: 20 residues processed: 92 average time/residue: 0.1648 time to fit residues: 22.4203 Evaluate side-chains 87 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 899 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 306 GLN A 538 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7895 Z= 0.221 Angle : 0.576 12.272 10712 Z= 0.300 Chirality : 0.044 0.288 1266 Planarity : 0.004 0.044 1394 Dihedral : 4.738 23.363 1117 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.89 % Allowed : 15.11 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.26), residues: 1047 helix: 0.75 (0.27), residues: 384 sheet: -2.21 (0.41), residues: 136 loop : -1.73 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.020 0.002 PHE A 29 TYR 0.012 0.001 TYR A 808 ARG 0.003 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8847 (tp) REVERT: A 880 MET cc_start: 0.8030 (mtt) cc_final: 0.7818 (mtt) outliers start: 22 outliers final: 15 residues processed: 90 average time/residue: 0.1664 time to fit residues: 21.9880 Evaluate side-chains 86 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7895 Z= 0.184 Angle : 0.552 11.657 10712 Z= 0.287 Chirality : 0.043 0.216 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.549 22.013 1117 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.15 % Allowed : 14.98 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 1047 helix: 0.87 (0.27), residues: 385 sheet: -2.14 (0.42), residues: 136 loop : -1.68 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.018 0.001 PHE A 29 TYR 0.028 0.001 TYR A 92 ARG 0.005 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8849 (tp) outliers start: 24 outliers final: 17 residues processed: 96 average time/residue: 0.1742 time to fit residues: 24.2041 Evaluate side-chains 93 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7895 Z= 0.196 Angle : 0.575 12.581 10712 Z= 0.293 Chirality : 0.043 0.184 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.525 22.126 1117 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.89 % Allowed : 16.95 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1047 helix: 0.98 (0.27), residues: 386 sheet: -2.21 (0.41), residues: 136 loop : -1.62 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.016 0.001 PHE A 29 TYR 0.011 0.001 TYR A 808 ARG 0.006 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8856 (tp) REVERT: A 880 MET cc_start: 0.7953 (mtt) cc_final: 0.7725 (mtt) outliers start: 22 outliers final: 18 residues processed: 91 average time/residue: 0.1642 time to fit residues: 22.7833 Evaluate side-chains 90 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN A 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7895 Z= 0.179 Angle : 0.568 13.498 10712 Z= 0.291 Chirality : 0.042 0.200 1266 Planarity : 0.004 0.040 1394 Dihedral : 4.448 21.863 1117 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.76 % Allowed : 17.48 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 1047 helix: 1.01 (0.27), residues: 386 sheet: -2.16 (0.42), residues: 136 loop : -1.59 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.017 0.001 PHE A 765 TYR 0.027 0.001 TYR A 92 ARG 0.006 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8859 (tp) outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 0.1621 time to fit residues: 22.1186 Evaluate side-chains 88 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7895 Z= 0.170 Angle : 0.580 13.957 10712 Z= 0.291 Chirality : 0.043 0.207 1266 Planarity : 0.004 0.039 1394 Dihedral : 4.340 21.335 1117 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.23 % Allowed : 18.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1047 helix: 1.11 (0.27), residues: 384 sheet: -2.00 (0.41), residues: 141 loop : -1.60 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.016 0.001 PHE A 505 TYR 0.010 0.001 TYR A 293 ARG 0.005 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8731 (tp) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.1614 time to fit residues: 22.3090 Evaluate side-chains 92 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7895 Z= 0.293 Angle : 0.644 14.336 10712 Z= 0.329 Chirality : 0.044 0.223 1266 Planarity : 0.004 0.037 1394 Dihedral : 4.657 23.461 1117 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.23 % Allowed : 18.66 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1047 helix: 1.11 (0.27), residues: 385 sheet: -2.05 (0.38), residues: 166 loop : -1.64 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.017 0.002 PHE A 505 TYR 0.011 0.001 TYR A 808 ARG 0.005 0.001 ARG A 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8862 (tp) outliers start: 17 outliers final: 14 residues processed: 93 average time/residue: 0.1723 time to fit residues: 23.4159 Evaluate side-chains 87 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 884 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.106758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085077 restraints weight = 18158.279| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.50 r_work: 0.3288 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7895 Z= 0.226 Angle : 0.618 14.140 10712 Z= 0.314 Chirality : 0.043 0.196 1266 Planarity : 0.004 0.038 1394 Dihedral : 4.674 23.102 1117 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.23 % Allowed : 18.53 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 1047 helix: 1.15 (0.27), residues: 384 sheet: -1.97 (0.41), residues: 141 loop : -1.68 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.003 0.001 HIS A 304 PHE 0.018 0.002 PHE A 505 TYR 0.010 0.001 TYR A 808 ARG 0.007 0.001 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.38 seconds wall clock time: 33 minutes 39.36 seconds (2019.36 seconds total)