Starting phenix.real_space_refine on Sat Nov 16 15:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/11_2024/8jpo_36485.cif" } resolution = 3.4 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 70 5.16 5 Cl 4 4.86 5 C 7430 2.51 5 N 1922 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.60, per 1000 atoms: 0.66 Number of scatterers: 11476 At special positions: 0 Unit cell: (92.9514, 96.301, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 70 16.00 P 6 15.00 Mg 2 11.99 O 2042 8.00 N 1922 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 8 sheets defined 65.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 123 removed outlier: 3.554A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 151 removed outlier: 3.605A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.825A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.618A pdb=" N GLY A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 201 through 214 removed outlier: 4.341A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.549A pdb=" N PHE A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 removed outlier: 4.087A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.681A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 366 removed outlier: 4.217A pdb=" N PHE A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 488 through 511 removed outlier: 3.760A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 3.816A pdb=" N ALA A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.852A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.793A pdb=" N ILE A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.605A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 123 removed outlier: 3.648A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.600A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.832A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.623A pdb=" N GLY B 186 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.558A pdb=" N MET B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.527A pdb=" N PHE B 232 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 removed outlier: 4.067A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.668A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 366 removed outlier: 4.152A pdb=" N PHE B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.636A pdb=" N VAL B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.650A pdb=" N GLN B 456 " --> pdb=" O GLN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 480 Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.751A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 removed outlier: 3.904A pdb=" N ALA B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.811A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.800A pdb=" N ILE B 604 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.658A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 removed outlier: 6.808A pdb=" N LEU A 835 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A 847 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 837 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 removed outlier: 6.782A pdb=" N LEU B 835 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 847 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 837 " --> pdb=" O VAL B 845 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1941 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: 3.45 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3614 1.34 - 1.47: 2886 1.47 - 1.59: 5122 1.59 - 1.71: 2 1.71 - 1.83: 110 Bond restraints: 11734 Sorted by residual: bond pdb=" C HIS B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" C HIS A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.42e+00 bond pdb=" CA GLY B 397 " pdb=" C GLY B 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.29e+00 bond pdb=" C VAL A 175 " pdb=" O VAL A 175 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.16e+00 bond pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 15186 1.28 - 2.56: 586 2.56 - 3.84: 117 3.84 - 5.12: 30 5.12 - 6.40: 9 Bond angle restraints: 15928 Sorted by residual: angle pdb=" N VAL A 162 " pdb=" CA VAL A 162 " pdb=" C VAL A 162 " ideal model delta sigma weight residual 112.96 107.99 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N VAL B 162 " pdb=" CA VAL B 162 " pdb=" C VAL B 162 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.96 -2.72 6.30e-01 2.52e+00 1.86e+01 angle pdb=" C GLY B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" C ILE A 159 " pdb=" CA ILE A 159 " pdb=" CB ILE A 159 " ideal model delta sigma weight residual 114.35 110.96 3.39 1.06e+00 8.90e-01 1.02e+01 ... (remaining 15923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 6212 14.64 - 29.27: 527 29.27 - 43.91: 140 43.91 - 58.55: 46 58.55 - 73.19: 21 Dihedral angle restraints: 6946 sinusoidal: 2748 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -148.19 62.19 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -147.05 61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1173 0.032 - 0.064: 466 0.064 - 0.096: 132 0.096 - 0.128: 64 0.128 - 0.160: 7 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB VAL B 242 " pdb=" CA VAL B 242 " pdb=" CG1 VAL B 242 " pdb=" CG2 VAL B 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1839 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 770 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 769 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 770 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 484 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 485 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.022 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2824 2.79 - 3.32: 11215 3.32 - 3.85: 18893 3.85 - 4.37: 22316 4.37 - 4.90: 39182 Nonbonded interactions: 94430 Sorted by model distance: nonbonded pdb=" O THR B 440 " pdb=" ND2 ASN B 444 " model vdw 2.267 3.120 nonbonded pdb=" O ASP A 603 " pdb=" NH1 ARG A 861 " model vdw 2.272 3.120 nonbonded pdb=" O ASP B 603 " pdb=" NH1 ARG B 861 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 440 " pdb=" ND2 ASN A 444 " model vdw 2.302 3.120 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.308 3.040 ... (remaining 94425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.650 Find NCS groups from input model: 0.520 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 0.037 11734 Z= 0.237 Angle : 0.628 6.396 15928 Z= 0.372 Chirality : 0.041 0.160 1842 Planarity : 0.005 0.040 1990 Dihedral : 12.938 73.186 4232 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.44 (0.23), residues: 1446 helix: 1.12 (0.18), residues: 896 sheet: -2.55 (0.85), residues: 24 loop : -0.96 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 851 PHE 0.014 0.001 PHE A 390 TYR 0.013 0.001 TYR A 781 ARG 0.005 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.225 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1932 time to fit residues: 32.6902 Evaluate side-chains 92 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 0.0050 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11734 Z= 0.208 Angle : 0.553 8.196 15928 Z= 0.283 Chirality : 0.040 0.158 1842 Planarity : 0.005 0.038 1990 Dihedral : 7.754 59.708 1642 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.40 % Allowed : 5.92 % Favored : 93.68 % 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 (0.23), residues: 1446 helix: 1.67 (0.18), residues: 902 sheet: -2.94 (0.80), residues: 24 loop : -0.80 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.003 0.001 HIS B 615 PHE 0.011 0.001 PHE A 351 TYR 0.026 0.001 TYR A 510 ARG 0.003 0.000 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.373 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.2042 time to fit residues: 34.0355 Evaluate side-chains 89 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11734 Z= 0.239 Angle : 0.537 7.426 15928 Z= 0.274 Chirality : 0.040 0.158 1842 Planarity : 0.004 0.039 1990 Dihedral : 6.952 53.070 1642 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.80 % Allowed : 7.44 % Favored : 91.76 % 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: 1.23 (0.23), residues: 1446 helix: 1.83 (0.18), residues: 902 sheet: -2.97 (0.81), residues: 24 loop : -0.81 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.003 0.001 HIS B 615 PHE 0.015 0.001 PHE A 101 TYR 0.015 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.431 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.2121 time to fit residues: 34.9812 Evaluate side-chains 98 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11734 Z= 0.206 Angle : 0.509 6.545 15928 Z= 0.260 Chirality : 0.039 0.158 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.734 54.668 1642 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.20 % Allowed : 8.00 % Favored : 90.80 % 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 (0.23), residues: 1446 helix: 1.94 (0.18), residues: 904 sheet: -3.06 (0.84), residues: 24 loop : -0.90 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.002 0.001 HIS B 615 PHE 0.013 0.001 PHE A 101 TYR 0.014 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.250 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.1945 time to fit residues: 34.6019 Evaluate side-chains 99 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11734 Z= 0.259 Angle : 0.543 8.941 15928 Z= 0.276 Chirality : 0.040 0.156 1842 Planarity : 0.004 0.038 1990 Dihedral : 6.695 55.858 1642 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.80 % Allowed : 9.60 % Favored : 89.60 % 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: 1.25 (0.23), residues: 1446 helix: 1.93 (0.18), residues: 900 sheet: -3.09 (0.86), residues: 24 loop : -0.96 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.003 0.001 HIS B 615 PHE 0.014 0.001 PHE B 101 TYR 0.015 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.522 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.2031 time to fit residues: 32.9392 Evaluate side-chains 97 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 141 optimal weight: 0.0070 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11734 Z= 0.177 Angle : 0.495 7.769 15928 Z= 0.253 Chirality : 0.038 0.157 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.463 60.023 1642 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.88 % Allowed : 9.92 % Favored : 89.20 % 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: 1.40 (0.23), residues: 1446 helix: 2.08 (0.18), residues: 900 sheet: -3.22 (0.87), residues: 24 loop : -0.95 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS B 579 PHE 0.012 0.001 PHE A 101 TYR 0.013 0.001 TYR A 781 ARG 0.002 0.000 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.308 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 0.2052 time to fit residues: 33.9567 Evaluate side-chains 100 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 0.0270 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 overall best weight: 1.0378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11734 Z= 0.165 Angle : 0.497 9.419 15928 Z= 0.251 Chirality : 0.038 0.156 1842 Planarity : 0.004 0.035 1990 Dihedral : 6.431 62.655 1642 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.96 % Allowed : 10.24 % Favored : 88.80 % 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: 1.50 (0.23), residues: 1446 helix: 2.17 (0.18), residues: 900 sheet: -3.27 (0.86), residues: 24 loop : -0.93 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 278 HIS 0.002 0.000 HIS B 515 PHE 0.012 0.001 PHE A 101 TYR 0.012 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 360 LYS cc_start: 0.8893 (mttt) cc_final: 0.8690 (mtmm) outliers start: 12 outliers final: 7 residues processed: 107 average time/residue: 0.2115 time to fit residues: 35.2892 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 128 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11734 Z= 0.167 Angle : 0.494 9.037 15928 Z= 0.250 Chirality : 0.038 0.156 1842 Planarity : 0.004 0.035 1990 Dihedral : 6.370 64.469 1642 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.96 % Allowed : 10.00 % Favored : 89.04 % 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: 1.56 (0.23), residues: 1446 helix: 2.24 (0.18), residues: 900 sheet: -3.27 (0.87), residues: 24 loop : -0.95 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 278 HIS 0.002 0.000 HIS B 515 PHE 0.012 0.001 PHE A 101 TYR 0.011 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 360 LYS cc_start: 0.8901 (mttt) cc_final: 0.8698 (mtmm) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.1883 time to fit residues: 31.6600 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11734 Z= 0.209 Angle : 0.523 9.367 15928 Z= 0.262 Chirality : 0.039 0.158 1842 Planarity : 0.004 0.036 1990 Dihedral : 6.485 63.355 1642 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.96 % Allowed : 10.08 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1446 helix: 2.16 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.002 0.001 HIS B 615 PHE 0.012 0.001 PHE B 101 TYR 0.012 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.416 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.2260 time to fit residues: 37.8142 Evaluate side-chains 104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11734 Z= 0.277 Angle : 0.557 9.357 15928 Z= 0.281 Chirality : 0.041 0.186 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.679 60.771 1642 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.88 % Allowed : 10.32 % Favored : 88.80 % 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: 1.38 (0.23), residues: 1446 helix: 2.06 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.003 0.001 HIS B 615 PHE 0.014 0.001 PHE A 351 TYR 0.013 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.297 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2150 time to fit residues: 34.9882 Evaluate side-chains 99 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.090793 restraints weight = 13503.535| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.42 r_work: 0.2931 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11734 Z= 0.143 Angle : 0.493 8.702 15928 Z= 0.247 Chirality : 0.038 0.157 1842 Planarity : 0.004 0.035 1990 Dihedral : 6.248 67.159 1642 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.40 % Allowed : 11.28 % Favored : 88.32 % 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: 1.61 (0.23), residues: 1446 helix: 2.26 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 278 HIS 0.002 0.000 HIS B 515 PHE 0.011 0.001 PHE B 97 TYR 0.010 0.001 TYR B 76 ARG 0.002 0.000 ARG A 861 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.38 seconds wall clock time: 39 minutes 36.91 seconds (2376.91 seconds total)