Starting phenix.real_space_refine on Fri Dec 8 04:52:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2023/6v4u_21048.pdb" } resolution = 3.8 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= 0.002 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4443 2.51 5 N 1262 2.21 5 O 1346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2475 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 324} Chain breaks: 7 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2075 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 221} Link IDs: {'PTRANS': 14, 'TRANS': 341} Chain breaks: 7 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 20, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 401 Chain: "B" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2524 Classifications: {'peptide': 421} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 231} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 11 Unresolved non-hydrogen bonds: 944 Unresolved non-hydrogen angles: 1200 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 19, 'PHE:plan': 14, 'GLU:plan': 24, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 541 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG C 347 " occ=0.81 ... (9 atoms not shown) pdb=" NH2 ARG C 347 " occ=0.71 Time building chain proxies: 4.42, per 1000 atoms: 0.62 Number of scatterers: 7074 At special positions: 0 Unit cell: (74.698, 122.964, 155.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1346 8.00 N 1262 7.00 C 4443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 40.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'A' and resid 55 through 69 removed outlier: 4.008A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.511A pdb=" N LEU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.631A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.632A pdb=" N THR A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 removed outlier: 4.180A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.779A pdb=" N TYR A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.953A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.702A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.862A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.472A pdb=" N MET A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 457 - end of helix Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'B' and resid 83 through 98 removed outlier: 5.647A pdb=" N TYR B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 217 removed outlier: 3.738A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.543A pdb=" N THR B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 359 Processing helix chain 'B' and resid 366 through 382 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.955A pdb=" N ALA B 723 " --> pdb=" O PHE B 719 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.592A pdb=" N LEU B 746 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.507A pdb=" N LEU B 750 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 751 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 752 " --> pdb=" O ALA B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 752' Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.936A pdb=" N MET B 775 " --> pdb=" O PRO B 771 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 777 " --> pdb=" O HIS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 832 Processing helix chain 'B' and resid 842 through 868 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 900 through 914 Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.638A pdb=" N LEU C 37 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 428 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 429 " --> pdb=" O THR C 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.835A pdb=" N ALA C 60 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 49 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 58 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 4.084A pdb=" N VAL C 117 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN C 127 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.631A pdb=" N ARG A 40 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 27 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 109 " --> pdb=" O TRP A 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'B' and resid 784 through 786 removed outlier: 8.209A pdb=" N LEU B 785 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 735 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 732 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 810 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 734 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 322 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.92 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: 2456 1.34 - 1.46: 1512 1.46 - 1.58: 3169 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7167 Sorted by residual: bond pdb=" N GLU A 442 " pdb=" CA GLU A 442 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.25e-02 6.40e+03 1.12e+00 bond pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.14e-01 bond pdb=" C LYS B 762 " pdb=" N PRO B 763 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.56e-01 bond pdb=" CA THR C 123 " pdb=" CB THR C 123 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.55e-01 bond pdb=" CA SER A 23 " pdb=" C SER A 23 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.11e-01 ... (remaining 7162 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 219 107.46 - 114.10: 4141 114.10 - 120.73: 2836 120.73 - 127.36: 2556 127.36 - 134.00: 65 Bond angle restraints: 9817 Sorted by residual: angle pdb=" N ILE A 224 " pdb=" CA ILE A 224 " pdb=" C ILE A 224 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.43e+00 angle pdb=" C GLU A 442 " pdb=" CA GLU A 442 " pdb=" CB GLU A 442 " ideal model delta sigma weight residual 109.62 114.66 -5.04 1.79e+00 3.12e-01 7.92e+00 angle pdb=" C LEU C 162 " pdb=" N ASP C 163 " pdb=" CA ASP C 163 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 angle pdb=" C THR C 122 " pdb=" N THR C 123 " pdb=" CA THR C 123 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" C MET C 255 " pdb=" N GLN C 256 " pdb=" CA GLN C 256 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.54e+00 ... (remaining 9812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.74: 3825 11.74 - 23.48: 238 23.48 - 35.22: 79 35.22 - 46.96: 22 46.96 - 58.70: 2 Dihedral angle restraints: 4166 sinusoidal: 999 harmonic: 3167 Sorted by residual: dihedral pdb=" CA GLN B 365 " pdb=" C GLN B 365 " pdb=" N HIS B 366 " pdb=" CA HIS B 366 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE B 85 " pdb=" C PHE B 85 " pdb=" N ASP B 86 " pdb=" CA ASP B 86 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU B 711 " pdb=" CB LEU B 711 " pdb=" CG LEU B 711 " pdb=" CD1 LEU B 711 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 712 0.028 - 0.056: 330 0.056 - 0.084: 95 0.084 - 0.112: 79 0.112 - 0.140: 10 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA ASP C 163 " pdb=" N ASP C 163 " pdb=" C ASP C 163 " pdb=" CB ASP C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL C 231 " pdb=" N VAL C 231 " pdb=" C VAL C 231 " pdb=" CB VAL C 231 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 402 " pdb=" N ILE C 402 " pdb=" C ILE C 402 " pdb=" CB ILE C 402 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1223 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 466 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 467 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 332 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 333 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.54e-01 pdb=" N PRO C 183 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.014 5.00e-02 4.00e+02 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1966 2.80 - 3.32: 6433 3.32 - 3.85: 11052 3.85 - 4.37: 11027 4.37 - 4.90: 19623 Nonbonded interactions: 50101 Sorted by model distance: nonbonded pdb=" O LEU B 750 " pdb=" OH TYR B 760 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP C 233 " pdb=" OG SER C 235 " model vdw 2.329 2.440 nonbonded pdb=" OD1 ASN C 232 " pdb=" OG1 THR C 290 " model vdw 2.329 2.440 nonbonded pdb=" N GLU C 409 " pdb=" O CYS C 422 " model vdw 2.345 2.520 nonbonded pdb=" O ALA B 706 " pdb=" OG1 THR B 748 " model vdw 2.356 2.440 ... (remaining 50096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.700 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: 0.000 Extract box with map and model: 3.160 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.700 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.002 0.021 7167 Z= 0.106 Angle : 0.471 8.209 9817 Z= 0.237 Chirality : 0.041 0.140 1226 Planarity : 0.003 0.029 1294 Dihedral : 9.643 58.703 2096 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -3.58 (0.23), residues: 1050 helix: 0.19 (0.23), residues: 411 sheet: -4.40 (0.39), residues: 76 loop : -4.35 (0.19), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 148 HIS 0.002 0.000 HIS C 404 PHE 0.008 0.001 PHE B 372 TYR 0.004 0.000 TYR B 99 ARG 0.001 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1817 time to fit residues: 36.3975 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0030 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.9570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 328 HIS B 337 GLN B 356 GLN B 708 GLN B 721 HIS B 848 GLN B 903 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7167 Z= 0.188 Angle : 0.546 8.160 9817 Z= 0.274 Chirality : 0.043 0.146 1226 Planarity : 0.004 0.069 1294 Dihedral : 3.012 14.716 1110 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.05 % Allowed : 17.11 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.25), residues: 1050 helix: 1.61 (0.26), residues: 411 sheet: -3.82 (0.36), residues: 104 loop : -4.09 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 431 HIS 0.008 0.001 HIS C 417 PHE 0.024 0.002 PHE B 345 TYR 0.020 0.002 TYR C 413 ARG 0.007 0.001 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.1772 time to fit residues: 26.7695 Evaluate side-chains 97 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0898 time to fit residues: 2.6622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 343 HIS B 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7167 Z= 0.355 Angle : 0.730 9.747 9817 Z= 0.385 Chirality : 0.048 0.201 1226 Planarity : 0.005 0.072 1294 Dihedral : 5.168 25.747 1110 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 4.48 % Allowed : 20.57 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.26), residues: 1050 helix: 1.19 (0.26), residues: 417 sheet: -3.68 (0.40), residues: 122 loop : -4.03 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 431 HIS 0.010 0.002 HIS B 846 PHE 0.028 0.003 PHE B 345 TYR 0.031 0.003 TYR A 124 ARG 0.008 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.1745 time to fit residues: 28.2220 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0677 time to fit residues: 2.4180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.0170 chunk 94 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7167 Z= 0.180 Angle : 0.601 9.356 9817 Z= 0.304 Chirality : 0.044 0.150 1226 Planarity : 0.004 0.066 1294 Dihedral : 4.079 17.719 1110 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.44 % Allowed : 25.66 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.26), residues: 1050 helix: 1.71 (0.26), residues: 418 sheet: -4.02 (0.37), residues: 112 loop : -3.91 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 148 HIS 0.004 0.001 HIS B 846 PHE 0.028 0.002 PHE C 132 TYR 0.015 0.002 TYR C 413 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.879 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 96 average time/residue: 0.1663 time to fit residues: 22.4230 Evaluate side-chains 83 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0647 time to fit residues: 1.5393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 94 optimal weight: 0.0170 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7167 Z= 0.178 Angle : 0.588 9.735 9817 Z= 0.295 Chirality : 0.044 0.154 1226 Planarity : 0.004 0.072 1294 Dihedral : 3.880 15.805 1110 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 4.28 % Allowed : 26.27 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 1050 helix: 1.91 (0.27), residues: 418 sheet: -3.90 (0.38), residues: 112 loop : -3.83 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 148 HIS 0.004 0.001 HIS B 846 PHE 0.031 0.002 PHE B 345 TYR 0.014 0.002 TYR C 413 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.791 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 106 average time/residue: 0.1653 time to fit residues: 24.8867 Evaluate side-chains 88 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0716 time to fit residues: 2.0600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7167 Z= 0.281 Angle : 0.687 10.116 9817 Z= 0.349 Chirality : 0.046 0.168 1226 Planarity : 0.004 0.077 1294 Dihedral : 4.534 20.408 1110 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 3.05 % Allowed : 28.11 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.27), residues: 1050 helix: 1.63 (0.27), residues: 419 sheet: -3.67 (0.39), residues: 117 loop : -3.80 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 210 HIS 0.007 0.001 HIS B 846 PHE 0.029 0.002 PHE C 132 TYR 0.015 0.002 TYR B 904 ARG 0.006 0.001 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.895 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.1704 time to fit residues: 24.2935 Evaluate side-chains 91 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0672 time to fit residues: 2.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 65 optimal weight: 0.0770 chunk 64 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 848 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7167 Z= 0.168 Angle : 0.622 9.647 9817 Z= 0.307 Chirality : 0.044 0.158 1226 Planarity : 0.004 0.076 1294 Dihedral : 3.969 17.390 1110 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 1.83 % Allowed : 29.53 % Favored : 68.64 % 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: -1.99 (0.27), residues: 1050 helix: 1.88 (0.27), residues: 418 sheet: -3.75 (0.39), residues: 117 loop : -3.70 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 210 HIS 0.004 0.001 HIS B 866 PHE 0.023 0.002 PHE C 132 TYR 0.026 0.002 TYR B 904 ARG 0.003 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.901 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.1695 time to fit residues: 22.0037 Evaluate side-chains 80 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0769 time to fit residues: 1.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7167 Z= 0.262 Angle : 0.686 10.313 9817 Z= 0.345 Chirality : 0.046 0.201 1226 Planarity : 0.005 0.083 1294 Dihedral : 4.526 19.019 1110 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 1.83 % Allowed : 30.75 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.27), residues: 1050 helix: 1.66 (0.27), residues: 419 sheet: -3.58 (0.40), residues: 117 loop : -3.71 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 148 HIS 0.006 0.001 HIS B 866 PHE 0.024 0.002 PHE C 132 TYR 0.021 0.002 TYR B 904 ARG 0.004 0.001 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.789 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.1820 time to fit residues: 23.5440 Evaluate side-chains 81 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0713 time to fit residues: 1.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7167 Z= 0.186 Angle : 0.648 9.883 9817 Z= 0.321 Chirality : 0.045 0.165 1226 Planarity : 0.004 0.080 1294 Dihedral : 4.228 22.929 1110 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.22 % Allowed : 31.16 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.27), residues: 1050 helix: 1.87 (0.27), residues: 413 sheet: -3.67 (0.39), residues: 117 loop : -3.60 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 148 HIS 0.013 0.001 HIS B 866 PHE 0.022 0.002 PHE C 132 TYR 0.023 0.001 TYR B 904 ARG 0.004 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.807 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 0.1683 time to fit residues: 19.8091 Evaluate side-chains 82 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0648 time to fit residues: 1.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7167 Z= 0.174 Angle : 0.644 11.571 9817 Z= 0.314 Chirality : 0.045 0.161 1226 Planarity : 0.004 0.078 1294 Dihedral : 3.979 17.522 1110 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 1.02 % Allowed : 30.35 % Favored : 68.64 % 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: -1.87 (0.27), residues: 1050 helix: 1.92 (0.27), residues: 419 sheet: -3.60 (0.40), residues: 117 loop : -3.61 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 148 HIS 0.008 0.001 HIS B 866 PHE 0.020 0.002 PHE C 132 TYR 0.024 0.001 TYR B 904 ARG 0.003 0.000 ARG C 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.816 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.1588 time to fit residues: 19.4243 Evaluate side-chains 78 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0662 time to fit residues: 1.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.116465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.100728 restraints weight = 24371.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.103230 restraints weight = 14708.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.104935 restraints weight = 10069.963| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7167 Z= 0.351 Angle : 0.783 11.500 9817 Z= 0.399 Chirality : 0.049 0.189 1226 Planarity : 0.006 0.125 1294 Dihedral : 5.293 26.359 1110 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.81 % Allowed : 31.36 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.27), residues: 1050 helix: 1.25 (0.27), residues: 420 sheet: -3.43 (0.40), residues: 132 loop : -3.65 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 431 HIS 0.007 0.002 HIS C 404 PHE 0.021 0.002 PHE C 132 TYR 0.027 0.002 TYR B 904 ARG 0.008 0.001 ARG C 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.43 seconds wall clock time: 29 minutes 15.29 seconds (1755.29 seconds total)