Starting phenix.real_space_refine on Tue Sep 24 05:54:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/09_2024/6v4u_21048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/09_2024/6v4u_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_21048/09_2024/6v4u_21048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/09_2024/6v4u_21048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/09_2024/6v4u_21048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/09_2024/6v4u_21048.cif" } 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. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.82, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.1 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: 0.69 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: 1.78 Time building geometry restraints manager: 1.97 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: 0.00 - 1.64: 9696 1.64 - 3.28: 89 3.28 - 4.93: 23 4.93 - 6.57: 7 6.57 - 8.21: 2 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 3.040 nonbonded pdb=" OD1 ASP C 233 " pdb=" OG SER C 235 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASN C 232 " pdb=" OG1 THR C 290 " model vdw 2.329 3.040 nonbonded pdb=" N GLU C 409 " pdb=" O CYS C 422 " model vdw 2.345 3.120 nonbonded pdb=" O ALA B 706 " pdb=" OG1 THR B 748 " model vdw 2.356 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- 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 : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.6796 (tppt) cc_final: 0.6446 (tppt) REVERT: C 211 ASP cc_start: 0.4780 (m-30) cc_final: 0.3466 (m-30) REVERT: A 385 PHE cc_start: 0.4738 (m-10) cc_final: 0.4289 (m-80) REVERT: A 417 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5697 (mm-30) REVERT: A 479 MET cc_start: 0.8090 (mmt) cc_final: 0.7830 (mpp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1720 time to fit residues: 34.4682 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 0.0060 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6518 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7167 Z= 0.242 Angle : 0.619 8.510 9817 Z= 0.317 Chirality : 0.044 0.207 1226 Planarity : 0.004 0.079 1294 Dihedral : 3.673 16.954 1110 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.26 % Allowed : 17.72 % Favored : 79.02 % 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: -2.63 (0.25), residues: 1050 helix: 1.36 (0.25), residues: 411 sheet: -3.78 (0.38), residues: 112 loop : -4.11 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 431 HIS 0.010 0.001 HIS C 417 PHE 0.025 0.002 PHE B 345 TYR 0.022 0.002 TYR A 124 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 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7258 (tppt) cc_final: 0.7051 (tppt) REVERT: A 385 PHE cc_start: 0.5103 (m-10) cc_final: 0.4820 (m-80) REVERT: A 417 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6116 (mm-30) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.1769 time to fit residues: 28.1619 Evaluate side-chains 97 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 0.0000 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 295 ASN ** 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: 0.6450 moved from start: 0.2782 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= 0.141 Angle : 0.525 8.812 9817 Z= 0.262 Chirality : 0.043 0.146 1226 Planarity : 0.004 0.066 1294 Dihedral : 3.168 16.767 1110 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.85 % Allowed : 22.00 % Favored : 75.15 % 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 (0.26), residues: 1050 helix: 1.93 (0.26), residues: 415 sheet: -3.80 (0.39), residues: 113 loop : -3.85 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 148 HIS 0.005 0.001 HIS C 83 PHE 0.023 0.001 PHE C 132 TYR 0.022 0.001 TYR C 413 ARG 0.005 0.001 ARG C 199 *********************** 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 111 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 HIS cc_start: 0.8148 (p90) cc_final: 0.7919 (p-80) REVERT: C 119 ASP cc_start: 0.7526 (t0) cc_final: 0.7299 (t0) REVERT: A 385 PHE cc_start: 0.5094 (m-10) cc_final: 0.4773 (m-80) REVERT: A 417 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6008 (mm-30) REVERT: B 911 LEU cc_start: 0.8842 (mt) cc_final: 0.8571 (mt) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 0.1614 time to fit residues: 23.8747 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7167 Z= 0.405 Angle : 0.736 8.797 9817 Z= 0.392 Chirality : 0.048 0.204 1226 Planarity : 0.005 0.073 1294 Dihedral : 4.839 24.419 1110 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 6.31 % Allowed : 21.38 % Favored : 72.30 % 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: 1.31 (0.26), residues: 417 sheet: -3.80 (0.38), residues: 124 loop : -3.86 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 431 HIS 0.008 0.002 HIS C 83 PHE 0.018 0.002 PHE A 84 TYR 0.028 0.003 TYR C 55 ARG 0.003 0.001 ARG C 347 *********************** 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 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: C 105 LEU cc_start: 0.7718 (pp) cc_final: 0.7113 (mp) REVERT: C 322 HIS cc_start: 0.4799 (OUTLIER) cc_final: 0.3676 (m90) REVERT: A 417 GLU cc_start: 0.6137 (mm-30) cc_final: 0.5813 (mm-30) REVERT: B 927 PHE cc_start: 0.4299 (m-80) cc_final: 0.4038 (m-80) outliers start: 31 outliers final: 18 residues processed: 122 average time/residue: 0.1674 time to fit residues: 28.1879 Evaluate side-chains 103 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 overall best weight: 1.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** 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: 0.6746 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7167 Z= 0.238 Angle : 0.635 9.416 9817 Z= 0.325 Chirality : 0.045 0.161 1226 Planarity : 0.004 0.072 1294 Dihedral : 4.314 19.777 1110 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 5.30 % Allowed : 25.66 % Favored : 69.04 % 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: -2.27 (0.27), residues: 1050 helix: 1.59 (0.27), residues: 422 sheet: -4.12 (0.37), residues: 104 loop : -3.82 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 148 HIS 0.006 0.001 HIS B 846 PHE 0.028 0.002 PHE C 132 TYR 0.017 0.002 TYR C 413 ARG 0.013 0.001 ARG C 160 *********************** 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 120 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: C 148 TRP cc_start: 0.7084 (p-90) cc_final: 0.6710 (p-90) REVERT: C 322 HIS cc_start: 0.5018 (OUTLIER) cc_final: 0.3669 (m90) REVERT: A 417 GLU cc_start: 0.5938 (mm-30) cc_final: 0.5554 (mm-30) REVERT: B 850 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7531 (mpp) outliers start: 26 outliers final: 15 residues processed: 111 average time/residue: 0.1656 time to fit residues: 25.9078 Evaluate side-chains 105 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 850 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0470 chunk 20 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** 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: 0.6649 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7167 Z= 0.165 Angle : 0.604 9.547 9817 Z= 0.296 Chirality : 0.044 0.176 1226 Planarity : 0.004 0.073 1294 Dihedral : 3.769 17.301 1110 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.07 % Allowed : 26.48 % 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: -1.86 (0.27), residues: 1050 helix: 2.03 (0.27), residues: 420 sheet: -3.78 (0.41), residues: 107 loop : -3.69 (0.23), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 118 HIS 0.003 0.001 HIS C 404 PHE 0.023 0.001 PHE A 397 TYR 0.023 0.002 TYR B 904 ARG 0.004 0.001 ARG C 160 *********************** 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 108 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 417 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5452 (mm-30) REVERT: B 850 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7652 (mpp) outliers start: 20 outliers final: 13 residues processed: 101 average time/residue: 0.1606 time to fit residues: 22.8761 Evaluate side-chains 97 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7167 Z= 0.224 Angle : 0.645 10.382 9817 Z= 0.321 Chirality : 0.045 0.162 1226 Planarity : 0.004 0.078 1294 Dihedral : 4.084 19.603 1110 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 4.89 % Allowed : 25.46 % Favored : 69.65 % 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: -1.88 (0.27), residues: 1050 helix: 1.85 (0.27), residues: 424 sheet: -3.68 (0.41), residues: 112 loop : -3.61 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 148 HIS 0.005 0.001 HIS B 846 PHE 0.020 0.002 PHE C 132 TYR 0.018 0.002 TYR B 904 ARG 0.010 0.001 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 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: C 37 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5480 (tt) REVERT: A 62 LEU cc_start: 0.9791 (mm) cc_final: 0.9585 (mp) REVERT: A 97 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 417 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5810 (mm-30) REVERT: B 850 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7632 (mpp) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.1569 time to fit residues: 24.7293 Evaluate side-chains 110 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7167 Z= 0.236 Angle : 0.669 10.207 9817 Z= 0.332 Chirality : 0.045 0.172 1226 Planarity : 0.004 0.079 1294 Dihedral : 4.274 17.465 1110 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 5.70 % Allowed : 26.07 % Favored : 68.23 % 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: -1.89 (0.27), residues: 1050 helix: 1.85 (0.27), residues: 424 sheet: -3.55 (0.41), residues: 117 loop : -3.64 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 148 HIS 0.005 0.001 HIS B 846 PHE 0.013 0.002 PHE C 297 TYR 0.026 0.002 TYR B 904 ARG 0.003 0.001 ARG C 160 *********************** 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 116 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8782 (t80) cc_final: 0.8458 (t80) REVERT: A 97 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 417 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6256 (mm-30) REVERT: B 850 MET cc_start: 0.7992 (mpp) cc_final: 0.7556 (mpp) REVERT: B 927 PHE cc_start: 0.4604 (m-80) cc_final: 0.4179 (m-80) outliers start: 28 outliers final: 23 residues processed: 108 average time/residue: 0.1657 time to fit residues: 24.9107 Evaluate side-chains 107 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 860 LEU 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: 9.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS B 884 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7167 Z= 0.399 Angle : 0.801 11.113 9817 Z= 0.415 Chirality : 0.048 0.187 1226 Planarity : 0.005 0.092 1294 Dihedral : 5.410 28.911 1110 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.29 % Favored : 83.71 % Rotamer: Outliers : 6.31 % Allowed : 25.46 % Favored : 68.23 % 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: -2.41 (0.26), residues: 1050 helix: 1.13 (0.26), residues: 428 sheet: -3.45 (0.40), residues: 125 loop : -3.78 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 431 HIS 0.011 0.002 HIS C 404 PHE 0.019 0.003 PHE A 84 TYR 0.018 0.002 TYR B 904 ARG 0.009 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 113 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: C 37 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5603 (tt) REVERT: C 105 LEU cc_start: 0.8151 (pp) cc_final: 0.7542 (mp) REVERT: A 61 PHE cc_start: 0.8889 (t80) cc_final: 0.8573 (t80) REVERT: A 97 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 385 PHE cc_start: 0.7211 (m-80) cc_final: 0.6933 (m-80) REVERT: B 850 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7407 (mpp) REVERT: B 854 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 927 PHE cc_start: 0.5295 (m-80) cc_final: 0.4859 (m-80) outliers start: 31 outliers final: 23 residues processed: 107 average time/residue: 0.1746 time to fit residues: 25.8425 Evaluate side-chains 104 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 860 LEU 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: 20.0000 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0040 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 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: 0.6884 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7167 Z= 0.262 Angle : 0.734 10.951 9817 Z= 0.368 Chirality : 0.046 0.175 1226 Planarity : 0.005 0.082 1294 Dihedral : 4.888 21.988 1110 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 4.89 % Allowed : 27.49 % 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: -2.27 (0.26), residues: 1050 helix: 1.29 (0.26), residues: 429 sheet: -3.50 (0.41), residues: 119 loop : -3.73 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 210 HIS 0.009 0.001 HIS B 866 PHE 0.015 0.002 PHE B 372 TYR 0.025 0.002 TYR B 904 ARG 0.005 0.001 ARG C 160 ********************** 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 108 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.751 Fit side-chains REVERT: C 105 LEU cc_start: 0.7915 (pp) cc_final: 0.7316 (mp) REVERT: A 61 PHE cc_start: 0.8830 (t80) cc_final: 0.8493 (t80) REVERT: A 97 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8596 (mp) REVERT: B 850 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: B 927 PHE cc_start: 0.5186 (m-80) cc_final: 0.4763 (m-80) outliers start: 24 outliers final: 20 residues processed: 103 average time/residue: 0.1737 time to fit residues: 24.9104 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 overall best weight: 1.6804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.118026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.102341 restraints weight = 24333.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104883 restraints weight = 14586.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.106658 restraints weight = 9922.879| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7167 Z= 0.273 Angle : 0.752 10.845 9817 Z= 0.375 Chirality : 0.047 0.181 1226 Planarity : 0.006 0.088 1294 Dihedral : 4.900 21.314 1110 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 4.68 % Allowed : 28.51 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.27), residues: 1050 helix: 1.32 (0.26), residues: 429 sheet: -3.33 (0.41), residues: 124 loop : -3.74 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 210 HIS 0.007 0.001 HIS B 866 PHE 0.035 0.002 PHE A 385 TYR 0.025 0.002 TYR B 904 ARG 0.006 0.001 ARG C 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.81 seconds wall clock time: 28 minutes 54.04 seconds (1734.04 seconds total)