Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 15:55:24 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2021/6v4u_21048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2021/6v4u_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_2021/6v4u_21048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2021/6v4u_21048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2021/6v4u_21048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/12_2021/6v4u_21048.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 4.56, per 1000 atoms: 0.64 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 Amimo 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 1.2 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: 0.35 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: 1.86 Time building geometry restraints manager: 2.97 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 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. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.410 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 21.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.040 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 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 % 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 *********************** 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 : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1773 time to fit residues: 35.7659 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1018 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.0392 ------------------------------------------------------------------------------- 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: 0.6400 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 7167 Z= 0.202 Angle : 0.580 8.199 9817 Z= 0.293 Chirality : 0.043 0.164 1226 Planarity : 0.006 0.103 1294 Dihedral : 3.182 14.401 1110 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.26), residues: 1050 helix: 1.51 (0.26), residues: 417 sheet: -3.74 (0.36), residues: 109 loop : -4.08 (0.22), residues: 524 *********************** 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 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.1752 time to fit residues: 27.6094 Evaluate side-chains 96 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0837 time to fit residues: 2.5633 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 7167 Z= 0.177 Angle : 0.535 8.102 9817 Z= 0.270 Chirality : 0.042 0.139 1226 Planarity : 0.005 0.097 1294 Dihedral : 3.110 16.256 1110 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 1.63 % 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: -2.04 (0.27), residues: 1050 helix: 2.01 (0.26), residues: 418 sheet: -3.86 (0.37), residues: 111 loop : -3.89 (0.23), residues: 521 *********************** 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 105 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.885 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 0.1610 time to fit residues: 23.0970 Evaluate side-chains 85 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0645 time to fit residues: 1.3591 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS A 128 HIS B 343 HIS B 848 GLN B 868 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 7167 Z= 0.562 Angle : 0.955 12.383 9817 Z= 0.510 Chirality : 0.052 0.187 1226 Planarity : 0.007 0.104 1294 Dihedral : 6.418 35.461 1110 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.67 % Favored : 83.24 % Rotamer Outliers : 6.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.17 (0.25), residues: 1050 helix: 0.37 (0.26), residues: 416 sheet: -3.59 (0.39), residues: 125 loop : -4.05 (0.23), residues: 509 *********************** 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 124 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.881 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 116 average time/residue: 0.1671 time to fit residues: 27.2518 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0678 time to fit residues: 3.3939 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.226 Angle : 0.670 9.793 9817 Z= 0.342 Chirality : 0.045 0.163 1226 Planarity : 0.006 0.109 1294 Dihedral : 4.825 20.240 1110 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 1050 helix: 1.33 (0.27), residues: 417 sheet: -3.85 (0.40), residues: 109 loop : -3.89 (0.23), residues: 524 *********************** 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 103 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 99 average time/residue: 0.1540 time to fit residues: 22.2616 Evaluate side-chains 84 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0741 time to fit residues: 1.4573 ------------------------------------------------------------------------------- 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: 0.0970 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** 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: 0.6681 moved from start: 0.5250 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= 0.170 Angle : 0.629 10.018 9817 Z= 0.309 Chirality : 0.044 0.156 1226 Planarity : 0.006 0.117 1294 Dihedral : 4.008 17.157 1110 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer Outliers : 2.85 % 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: -2.08 (0.27), residues: 1050 helix: 1.85 (0.27), residues: 422 sheet: -4.09 (0.37), residues: 110 loop : -3.78 (0.23), residues: 518 *********************** 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: 14 poor density : 90 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.1509 time to fit residues: 22.0622 Evaluate side-chains 85 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0701 time to fit residues: 1.9679 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** 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: 0.6683 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7167 Z= 0.178 Angle : 0.631 11.515 9817 Z= 0.308 Chirality : 0.044 0.157 1226 Planarity : 0.006 0.116 1294 Dihedral : 3.890 18.649 1110 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 2.04 % 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: -1.93 (0.27), residues: 1050 helix: 1.91 (0.27), residues: 424 sheet: -3.92 (0.37), residues: 116 loop : -3.66 (0.24), residues: 510 *********************** 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 95 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1754 time to fit residues: 23.4621 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1089 time to fit residues: 2.0919 ------------------------------------------------------------------------------- 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: 0.0670 chunk 31 optimal weight: 0.0170 chunk 20 optimal weight: 0.0010 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 100 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 overall best weight: 0.0458 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5085 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= 0.160 Angle : 0.635 12.887 9817 Z= 0.303 Chirality : 0.044 0.146 1226 Planarity : 0.005 0.119 1294 Dihedral : 3.599 18.117 1110 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 0.41 % 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: -1.74 (0.27), residues: 1050 helix: 2.13 (0.27), residues: 425 sheet: -3.68 (0.39), residues: 116 loop : -3.67 (0.24), residues: 509 *********************** 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 88 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.857 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.2018 time to fit residues: 26.0358 Evaluate side-chains 77 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0954 time to fit residues: 1.4054 ------------------------------------------------------------------------------- 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: 10.0000 chunk 100 optimal weight: 0.0040 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.0010 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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** A 65 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 7167 Z= 0.217 Angle : 0.664 13.336 9817 Z= 0.321 Chirality : 0.045 0.184 1226 Planarity : 0.006 0.126 1294 Dihedral : 3.972 17.298 1110 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.27), residues: 1050 helix: 1.98 (0.27), residues: 424 sheet: -3.65 (0.38), residues: 121 loop : -3.59 (0.24), residues: 505 *********************** 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 83 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 0.1442 time to fit residues: 17.5068 Evaluate side-chains 75 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0643 time to fit residues: 1.2288 ------------------------------------------------------------------------------- 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: 10.0000 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 99 optimal weight: 0.0470 chunk 86 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.0570 overall best weight: 0.2414 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 7167 Z= 0.163 Angle : 0.652 14.152 9817 Z= 0.309 Chirality : 0.044 0.150 1226 Planarity : 0.006 0.129 1294 Dihedral : 3.656 17.678 1110 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.20 % 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: -1.64 (0.28), residues: 1050 helix: 2.13 (0.27), residues: 425 sheet: -3.51 (0.40), residues: 116 loop : -3.56 (0.24), residues: 509 ********************** 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 82 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.860 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1376 time to fit residues: 17.4038 Evaluate side-chains 80 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0644 time to fit residues: 1.2626 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.108276 restraints weight = 24066.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.110901 restraints weight = 14524.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112758 restraints weight = 9910.946| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.182 Angle : 0.633 10.172 9817 Z= 0.306 Chirality : 0.044 0.160 1226 Planarity : 0.006 0.120 1294 Dihedral : 3.748 18.078 1110 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer Outliers : 0.20 % 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: -1.58 (0.28), residues: 1050 helix: 2.15 (0.27), residues: 425 sheet: -3.42 (0.40), residues: 121 loop : -3.51 (0.25), residues: 504 =============================================================================== Job complete usr+sys time: 1507.22 seconds wall clock time: 27 minutes 59.85 seconds (1679.85 seconds total)