Starting phenix.real_space_refine (version: dev) on Mon Apr 4 15:57:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/04_2022/6djp_7939.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7307 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 2979 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 28, 'TRANS': 564} Unresolved non-hydrogen bonds: 1693 Unresolved non-hydrogen angles: 2167 Unresolved non-hydrogen dihedrals: 1414 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 4, 'TYR:plan': 26, 'ASN:plan1': 18, 'TRP:plan': 5, 'ASP:plan': 47, 'PHE:plan': 37, 'GLU:plan': 22, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1027 Chain: "B" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1791 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1013 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 12, 'ASN:plan1': 22, 'TRP:plan': 2, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 22, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 536 Chain: "C" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 239 Chain: "D" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 536 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 152 Chain: "E" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 569 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 209 Chain: "F" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 102, 'PCIS': 1} Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 170 Unusual residues: {'BMA': 1, 'NAG': 9, 'MAN': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 137 Unusual residues: {'BMA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.41, per 1000 atoms: 0.74 Number of scatterers: 7307 At special positions: 0 Unit cell: (96.86, 126.92, 172.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1518 8.00 N 1421 7.00 C 4368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A1007 " - " MAN A1008 " ALPHA1-4 " MAN A1009 " - " MAN A1010 " ALPHA1-6 " BMA A1007 " - " MAN A1009 " BETA1-4 " NAG A1001 " - " NAG A1002 " " NAG A1003 " - " NAG A1004 " " NAG A1005 " - " NAG A1006 " " NAG A1006 " - " BMA A1007 " " NAG A1012 " - " NAG A1013 " " NAG B 702 " - " NAG B 703 " " NAG B 704 " - " NAG B 705 " " NAG B 706 " - " NAG B 707 " " NAG B 708 " - " NAG B 709 " " NAG B 709 " - " BMA B 710 " NAG-ASN " NAG A1001 " - " ASN A 44 " " NAG A1003 " - " ASN A 260 " " NAG A1005 " - " ASN A 266 " " NAG A1011 " - " ASN A 524 " " NAG A1012 " - " ASN A 585 " " NAG B 701 " - " ASN B 379 " " NAG B 702 " - " ASN B 191 " " NAG B 704 " - " ASN B 360 " " NAG B 706 " - " ASN B 389 " " NAG B 708 " - " ASN B 414 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 10.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 136 removed outlier: 4.805A pdb=" N LYS B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.980A pdb=" N HIS B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 344 removed outlier: 4.322A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.309A pdb=" N ALA D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.019A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.008A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 3.608A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.749A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.658A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283 removed outlier: 3.751A pdb=" N SER A 279 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 5.935A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AB6, first strand: chain 'B' and resid 81 through 84 removed outlier: 5.559A pdb=" N ILE B 419 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA B 406 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE B 421 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 404 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 97 Processing sheet with id=AB8, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.260A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.379A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC6, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.840A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.084A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.484A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.484A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1422 1.29 - 1.36: 1416 1.36 - 1.43: 65 1.43 - 1.51: 1855 1.51 - 1.58: 2604 Bond restraints: 7362 Sorted by residual: bond pdb=" C GLY B 376 " pdb=" N CYS B 377 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.45e-02 4.76e+03 3.75e+01 bond pdb=" C4 NAG A1002 " pdb=" O4 NAG A1002 " ideal model delta sigma weight residual 1.423 1.463 -0.040 1.00e-02 1.00e+04 1.58e+01 bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" C GLU B 385 " pdb=" N VAL B 386 " ideal model delta sigma weight residual 1.329 1.393 -0.064 1.69e-02 3.50e+03 1.46e+01 bond pdb=" C3 NAG A1002 " pdb=" C4 NAG A1002 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.00e-02 1.00e+04 1.45e+01 ... (remaining 7357 not shown) Histogram of bond angle deviations from ideal: 99.17 - 105.98: 331 105.98 - 112.80: 3672 112.80 - 119.62: 2336 119.62 - 126.43: 3863 126.43 - 133.25: 57 Bond angle restraints: 10259 Sorted by residual: angle pdb=" N ARG F 61 " pdb=" CA ARG F 61 " pdb=" C ARG F 61 " ideal model delta sigma weight residual 114.56 102.74 11.82 1.27e+00 6.20e-01 8.66e+01 angle pdb=" C MET A 400 " pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 119.66 126.19 -6.53 7.30e-01 1.88e+00 8.01e+01 angle pdb=" N TYR F 32 " pdb=" CA TYR F 32 " pdb=" C TYR F 32 " ideal model delta sigma weight residual 108.60 121.42 -12.82 1.46e+00 4.69e-01 7.71e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 128.35 -8.79 1.02e+00 9.61e-01 7.43e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.33 -8.77 1.02e+00 9.61e-01 7.40e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.89: 4175 9.89 - 19.79: 112 19.79 - 29.68: 8 29.68 - 39.57: 1 39.57 - 49.46: 2 Dihedral angle restraints: 4298 sinusoidal: 364 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASN C 61 " pdb=" C ASN C 61 " pdb=" N PRO C 62 " pdb=" CA PRO C 62 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLY A 173 " pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N ASN A 524 " pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " pdb=" CG ASN A 524 " ideal model delta sinusoidal sigma weight residual -60.00 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 4295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1017 0.075 - 0.150: 302 0.150 - 0.225: 55 0.225 - 0.300: 11 0.300 - 0.376: 4 Chirality restraints: 1389 Sorted by residual: chirality pdb=" C1 NAG B 707 " pdb=" O4 NAG B 706 " pdb=" C2 NAG B 707 " pdb=" O5 NAG B 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.92e+01 chirality pdb=" C1 MAN A1010 " pdb=" O4 MAN A1009 " pdb=" C2 MAN A1010 " pdb=" O5 MAN A1010 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-02 2.50e+03 4.09e+01 chirality pdb=" C1 BMA B 710 " pdb=" O4 NAG B 709 " pdb=" C2 BMA B 710 " pdb=" O5 BMA B 710 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.69e+01 ... (remaining 1386 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 706 " -0.051 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" C7 NAG B 706 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG B 706 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B 706 " 0.068 2.00e-02 2.50e+03 pdb=" O7 NAG B 706 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " 0.034 2.00e-02 2.50e+03 3.45e-02 1.49e+01 pdb=" CG ASN A 524 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.053 2.00e-02 2.50e+03 pdb=" C1 NAG A1011 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 709 " 0.040 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" C7 NAG B 709 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 709 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG B 709 " -0.051 2.00e-02 2.50e+03 pdb=" O7 NAG B 709 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2968 2.87 - 3.38: 6035 3.38 - 3.89: 9738 3.89 - 4.39: 9675 4.39 - 4.90: 16905 Nonbonded interactions: 45321 Sorted by model distance: nonbonded pdb=" N ARG F 61 " pdb=" N PHE F 62 " model vdw 2.368 2.560 nonbonded pdb=" N SER C 59 " pdb=" O SER C 59 " model vdw 2.447 2.496 nonbonded pdb=" O4 NAG A1002 " pdb=" O6 NAG A1002 " model vdw 2.450 2.440 nonbonded pdb=" N GLU A 367 " pdb=" O GLU A 367 " model vdw 2.457 2.496 nonbonded pdb=" O4 NAG B 707 " pdb=" O6 NAG B 707 " model vdw 2.457 2.440 ... (remaining 45316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4368 2.51 5 N 1421 2.21 5 O 1518 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 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 26.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 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 : 0.011 0.089 7362 Z= 0.853 Angle : 1.996 17.240 10259 Z= 1.372 Chirality : 0.076 0.376 1389 Planarity : 0.009 0.042 1476 Dihedral : 5.342 49.465 1750 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.74 (0.22), residues: 1379 helix: -1.92 (0.42), residues: 107 sheet: -0.01 (0.22), residues: 477 loop : -0.52 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.775 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0789 time to fit residues: 5.5653 Evaluate side-chains 29 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 7362 Z= 0.258 Angle : 0.674 13.567 10259 Z= 0.378 Chirality : 0.049 0.306 1389 Planarity : 0.005 0.051 1476 Dihedral : 5.668 28.421 1544 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.35 (0.22), residues: 1379 helix: -0.40 (0.52), residues: 97 sheet: 0.08 (0.22), residues: 504 loop : -0.35 (0.23), residues: 778 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.787 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0753 time to fit residues: 5.4070 Evaluate side-chains 30 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.190 7362 Z= 0.891 Angle : 1.440 20.904 10259 Z= 0.857 Chirality : 0.063 0.392 1389 Planarity : 0.010 0.088 1476 Dihedral : 11.489 59.604 1544 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 1.31 % Allowed : 14.43 % Favored : 84.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 1.44 % 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: -3.00 (0.21), residues: 1379 helix: -3.08 (0.41), residues: 86 sheet: -0.84 (0.24), residues: 431 loop : -2.64 (0.19), residues: 862 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.803 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0718 time to fit residues: 5.0837 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 7362 Z= 0.242 Angle : 0.697 12.707 10259 Z= 0.389 Chirality : 0.050 0.435 1389 Planarity : 0.005 0.044 1476 Dihedral : 7.303 53.308 1544 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.17 (0.22), residues: 1379 helix: -0.76 (0.52), residues: 86 sheet: -0.85 (0.23), residues: 493 loop : -1.95 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.885 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0687 time to fit residues: 4.7811 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.9434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.288 7362 Z= 0.932 Angle : 1.403 19.911 10259 Z= 0.835 Chirality : 0.061 0.376 1389 Planarity : 0.010 0.065 1476 Dihedral : 11.495 47.691 1544 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 33.51 Ramachandran Plot: Outliers : 2.18 % Allowed : 21.17 % Favored : 76.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 1.89 % 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: -4.32 (0.20), residues: 1379 helix: -3.80 (0.35), residues: 80 sheet: -1.68 (0.26), residues: 388 loop : -3.56 (0.17), residues: 911 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.807 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0678 time to fit residues: 4.6362 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.8727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 7362 Z= 0.230 Angle : 0.712 13.803 10259 Z= 0.398 Chirality : 0.050 0.433 1389 Planarity : 0.006 0.047 1476 Dihedral : 7.763 57.712 1544 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.38 (0.21), residues: 1379 helix: -1.42 (0.48), residues: 85 sheet: -1.66 (0.23), residues: 477 loop : -2.82 (0.20), residues: 817 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.862 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0717 time to fit residues: 4.9220 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.9230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.150 7362 Z= 0.473 Angle : 0.881 14.612 10259 Z= 0.503 Chirality : 0.051 0.390 1389 Planarity : 0.006 0.053 1476 Dihedral : 8.509 54.916 1544 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 19.22 % Favored : 80.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.68 (0.21), residues: 1379 helix: -1.75 (0.47), residues: 85 sheet: -1.61 (0.25), residues: 421 loop : -3.13 (0.19), residues: 873 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.788 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0679 time to fit residues: 4.6927 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 1.0152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.237 7362 Z= 0.613 Angle : 1.048 17.902 10259 Z= 0.612 Chirality : 0.053 0.403 1389 Planarity : 0.008 0.059 1476 Dihedral : 9.903 45.948 1544 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 23.71 % Favored : 76.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.13 % 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: -4.36 (0.20), residues: 1379 helix: -2.69 (0.44), residues: 84 sheet: -1.93 (0.25), residues: 406 loop : -3.62 (0.18), residues: 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.887 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0700 time to fit residues: 4.8138 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 1.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.250 7362 Z= 0.682 Angle : 1.113 17.736 10259 Z= 0.651 Chirality : 0.055 0.420 1389 Planarity : 0.008 0.066 1476 Dihedral : 10.360 47.879 1544 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 24.73 % Favored : 74.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 1.21 % 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: -4.86 (0.19), residues: 1379 helix: -3.05 (0.41), residues: 84 sheet: -2.31 (0.25), residues: 393 loop : -3.94 (0.17), residues: 902 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0676 time to fit residues: 4.6837 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 1.0298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7362 Z= 0.210 Angle : 0.680 13.841 10259 Z= 0.381 Chirality : 0.050 0.451 1389 Planarity : 0.006 0.055 1476 Dihedral : 7.534 57.186 1544 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.51 % Favored : 89.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.90 (0.21), residues: 1379 helix: -0.56 (0.54), residues: 87 sheet: -2.21 (0.24), residues: 435 loop : -3.18 (0.19), residues: 857 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.869 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0684 time to fit residues: 4.6904 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064395 restraints weight = 44895.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064951 restraints weight = 37328.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065551 restraints weight = 31455.168| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 1.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.241 7362 Z= 0.630 Angle : 1.031 17.618 10259 Z= 0.600 Chirality : 0.053 0.430 1389 Planarity : 0.008 0.059 1476 Dihedral : 9.540 48.873 1544 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.65 % Allowed : 24.58 % Favored : 74.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: -4.67 (0.20), residues: 1379 helix: -2.51 (0.42), residues: 90 sheet: -2.36 (0.24), residues: 415 loop : -3.77 (0.18), residues: 874 =============================================================================== Job complete usr+sys time: 1147.74 seconds wall clock time: 21 minutes 29.49 seconds (1289.49 seconds total)