Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 16:49:16 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5r_11648/01_2021/7a5r_11648.pdb" } resolution = 3.7 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= 0.038 Set model interpretation parameters 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 Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 10608 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 198, 'PCIS': 2} Chain breaks: 1 Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 190, 'PCIS': 3} Chain breaks: 2 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "B" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "M" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 190, 'PCIS': 3} Chain breaks: 2 Chain: "I" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 198, 'PCIS': 2} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.14, per 1000 atoms: 0.58 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Number of scatterers: 10608 At special positions: 0 Unit cell: (138.049, 166.311, 71.742, 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 40 16.00 O 2060 8.00 N 1748 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 343 " " NAG D 1 " - " ASN B 343 " Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 6.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.238A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 4.61 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: 3324 1.34 - 1.46: 2768 1.46 - 1.58: 4730 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10870 Sorted by residual: bond pdb=" N LEU H 174 " pdb=" CA LEU H 174 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.14e+00 bond pdb=" N LEU I 174 " pdb=" CA LEU I 174 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" CG PRO H 153 " pdb=" CD PRO H 153 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.25e+00 bond pdb=" CG PRO I 153 " pdb=" CD PRO I 153 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.25e+00 bond pdb=" CB PRO H 153 " pdb=" CG PRO H 153 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.08e+00 ... (remaining 10865 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 388 106.60 - 113.45: 5794 113.45 - 120.30: 3770 120.30 - 127.15: 4704 127.15 - 134.00: 130 Bond angle restraints: 14786 Sorted by residual: angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 111.91 116.08 -4.17 1.52e+00 4.33e-01 7.53e+00 angle pdb=" CA ILE M 2 " pdb=" CB ILE M 2 " pdb=" CG1 ILE M 2 " ideal model delta sigma weight residual 110.40 115.06 -4.66 1.70e+00 3.46e-01 7.51e+00 angle pdb=" CA ILE L 2 " pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 111.91 116.05 -4.14 1.52e+00 4.33e-01 7.42e+00 angle pdb=" C ILE A 332 " pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 122.08 126.78 -4.70 1.84e+00 2.95e-01 6.53e+00 ... (remaining 14781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5839 17.87 - 35.75: 497 35.75 - 53.62: 98 53.62 - 71.49: 22 71.49 - 89.37: 6 Dihedral angle restraints: 6462 sinusoidal: 2524 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.54 -36.54 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 200 " pdb=" CB CYS I 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.53 -36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -122.12 36.12 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 6459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 973 0.035 - 0.069: 405 0.069 - 0.104: 184 0.104 - 0.138: 81 0.138 - 0.173: 9 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB ILE M 34 " pdb=" CA ILE M 34 " pdb=" CG1 ILE M 34 " pdb=" CG2 ILE M 34 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR I 91 " pdb=" CA THR I 91 " pdb=" OG1 THR I 91 " pdb=" CG2 THR I 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1649 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO H 153 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 152 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO I 153 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 512 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C VAL B 512 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL B 512 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 513 " -0.010 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1233 2.75 - 3.29: 9288 3.29 - 3.83: 15432 3.83 - 4.36: 17584 4.36 - 4.90: 32591 Nonbonded interactions: 76128 Sorted by model distance: nonbonded pdb=" OG SER M 127 " pdb=" NZ LYS I 218 " model vdw 2.218 2.520 nonbonded pdb=" OG SER M 120 " pdb=" OD1 ASN M 143 " model vdw 2.381 2.440 nonbonded pdb=" OG SER L 120 " pdb=" OD1 ASN L 143 " model vdw 2.381 2.440 nonbonded pdb=" NZ LYS H 218 " pdb=" OG SER L 127 " model vdw 2.405 2.520 nonbonded pdb=" O LEU H 174 " pdb=" CD1 LEU H 174 " model vdw 2.418 3.460 ... (remaining 76123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 10608 10608 False True 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 40 5.16 5 C 6760 2.51 5 N 1748 2.21 5 O 2060 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables 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: 3.810 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.050 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.050 Process input model: 34.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.052 10870 Angle : 0.828 10.648 14786 Chirality : 0.049 0.173 1652 Planarity : 0.005 0.051 1882 Dihedral : 13.959 89.368 3894 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.26 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.97 (0.22), residues: 1318 helix: -2.70 (0.69), residues: 52 sheet: 0.16 (0.24), residues: 482 loop : -2.31 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.204 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.2905 time to fit residues: 54.1304 Evaluate side-chains 119 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 115 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3652 time to fit residues: 5.8945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 77 ASN H 203 ASN L 35 ASN L 44 GLN L 106 GLN A 49 HIS A 271 GLN A 321 GLN A 422 ASN B 271 GLN B 422 ASN B 493 GLN M 35 ASN M 44 GLN M 106 GLN I 39 GLN I 77 ASN I 203 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.050 10870 Angle : 0.695 10.213 14786 Chirality : 0.047 0.161 1652 Planarity : 0.005 0.042 1882 Dihedral : 4.931 19.759 1486 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1318 helix: -3.10 (0.73), residues: 40 sheet: 0.45 (0.23), residues: 528 loop : -1.98 (0.20), residues: 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.442 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 127 average time/residue: 0.2606 time to fit residues: 35.2406 Evaluate side-chains 97 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 121 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 542 ASN B 321 GLN B 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.034 10870 Angle : 0.613 8.590 14786 Chirality : 0.044 0.145 1652 Planarity : 0.004 0.040 1882 Dihedral : 4.548 18.868 1486 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.28 (0.22), residues: 1318 helix: -3.40 (0.55), residues: 64 sheet: 0.43 (0.22), residues: 546 loop : -1.71 (0.21), residues: 708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2944 time to fit residues: 39.6481 Evaluate side-chains 99 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 GLN L 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.045 10870 Angle : 0.661 9.308 14786 Chirality : 0.046 0.149 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.850 17.480 1486 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.27 (0.22), residues: 1318 helix: -4.02 (0.50), residues: 52 sheet: 0.59 (0.23), residues: 526 loop : -1.77 (0.21), residues: 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.373 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2674 time to fit residues: 34.2360 Evaluate side-chains 101 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 53 optimal weight: 0.0170 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN A 321 GLN B 321 GLN M 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.040 10870 Angle : 0.619 8.466 14786 Chirality : 0.045 0.144 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.695 18.733 1486 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.33 (0.22), residues: 1318 helix: -4.16 (0.46), residues: 52 sheet: 0.59 (0.23), residues: 512 loop : -1.80 (0.20), residues: 754 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.491 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2597 time to fit residues: 33.1332 Evaluate side-chains 99 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.0020 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN M 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.033 10870 Angle : 0.587 8.285 14786 Chirality : 0.044 0.141 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.496 18.989 1486 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.19 (0.22), residues: 1318 helix: -4.31 (0.42), residues: 52 sheet: 0.67 (0.23), residues: 512 loop : -1.66 (0.20), residues: 754 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.423 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.2521 time to fit residues: 33.2926 Evaluate side-chains 96 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 94 optimal weight: 0.0000 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN L 130 GLN A 321 GLN B 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.033 10870 Angle : 0.590 7.888 14786 Chirality : 0.044 0.145 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.445 21.497 1486 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1318 helix: -4.12 (0.51), residues: 40 sheet: 0.69 (0.23), residues: 512 loop : -1.61 (0.20), residues: 766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.393 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2464 time to fit residues: 33.2960 Evaluate side-chains 97 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.034 10870 Angle : 0.589 7.660 14786 Chirality : 0.044 0.142 1652 Planarity : 0.004 0.050 1882 Dihedral : 4.428 21.386 1486 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1318 helix: -4.24 (0.49), residues: 40 sheet: 0.81 (0.24), residues: 478 loop : -1.60 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.241 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2441 time to fit residues: 32.2835 Evaluate side-chains 100 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 72 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 0.0010 chunk 127 optimal weight: 1.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN A 321 GLN B 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.034 10870 Angle : 0.559 7.497 14786 Chirality : 0.043 0.153 1652 Planarity : 0.004 0.049 1882 Dihedral : 4.185 19.354 1486 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1318 helix: -4.11 (0.51), residues: 40 sheet: 0.91 (0.24), residues: 478 loop : -1.49 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.429 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2409 time to fit residues: 33.0580 Evaluate side-chains 102 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 35 ASN A 321 GLN B 49 HIS M 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.061 10870 Angle : 0.715 10.498 14786 Chirality : 0.048 0.149 1652 Planarity : 0.005 0.062 1882 Dihedral : 5.011 23.355 1486 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.21 (0.22), residues: 1318 helix: -3.93 (0.98), residues: 16 sheet: 0.78 (0.24), residues: 472 loop : -1.82 (0.19), residues: 830 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield and 0 Emsley and 1318 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.501 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2679 time to fit residues: 32.2504 Evaluate side-chains 87 residues out of total 1190 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN A 321 GLN B 321 GLN M 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139461 restraints weight = 16920.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141605 restraints weight = 11949.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143129 restraints weight = 9239.442| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.041 10870 ANGLE : 0.625 8.527 14786 CHIRALITY : 0.045 0.147 1652 PLANARITY : 0.005 0.063 1882 DIHEDRAL : 4.694 20.921 1486 MIN NONBONDED DISTANCE : 2.265 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.59 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.78 % FAVORED : 95.22 % ROTAMER OUTLIERS : 0.17 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 11.90 % 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: -1.14 (0.22), RESIDUES: 1318 HELIX: -4.26 (0.61), RESIDUES: 28 SHEET: 0.63 (0.24), RESIDUES: 512 LOOP : -1.68 (0.20), RESIDUES: 778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.041 10870 Angle : 0.625 8.527 14786 Chirality : 0.045 0.147 1652 Planarity : 0.005 0.063 1882 Dihedral : 4.694 20.921 1486 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -1.14 (0.22), residues: 1318 helix: -4.26 (0.61), residues: 28 sheet: 0.63 (0.24), residues: 512 loop : -1.68 (0.20), residues: 778 =============================================================================== Job complete usr+sys time: 2182.00 seconds wall clock time: 40 minutes 47.45 seconds (2447.45 seconds total)