Starting phenix.real_space_refine (version: dev) on Mon Feb 20 14:57:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/02_2023/7l49_23158.pdb" } resolution = 3.1 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= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 599 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC%5*END:plan2': 1, ' DC%5*END:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2877 Classifications: {'RNA': 135} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 120} Chain breaks: 2 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3858 SG CYS A 478 7.021 61.788 44.308 1.00 37.58 S ATOM 4048 SG CYS A 500 10.720 61.502 41.558 1.00 40.36 S ATOM 364 SG CYS A 50 53.252 98.716 77.958 1.00 42.34 S ATOM 502 SG CYS A 69 57.157 99.263 78.476 1.00 31.65 S ATOM 527 SG CYS A 72 55.385 96.180 79.439 1.00 31.06 S ATOM 8043 SG CYS B 478 59.449 58.052 9.211 1.00 58.65 S ATOM 8229 SG CYS B 500 56.592 59.678 11.519 1.00 65.09 S Time building chain proxies: 7.48, per 1000 atoms: 0.60 Number of scatterers: 12414 At special positions: 0 Unit cell: (102.9, 121.8, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 190 15.00 O 2779 8.00 N 2218 7.00 C 7186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 478 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 500 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 46.0% alpha, 10.5% beta 59 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 Processing helix chain 'A' and resid 52 through 58 removed outlier: 4.153A pdb=" N VAL A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.678A pdb=" N ARG A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.931A pdb=" N TYR A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.575A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.644A pdb=" N ASN A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.901A pdb=" N GLU A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 382 through 414 removed outlier: 3.707A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 518 removed outlier: 3.597A pdb=" N ALA A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 removed outlier: 3.557A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.968A pdb=" N VAL B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.747A pdb=" N ALA B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.626A pdb=" N TYR B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.664A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.958A pdb=" N PHE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.569A pdb=" N SER B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 4.198A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.612A pdb=" N GLU B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.991A pdb=" N LYS B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 414 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 444 through 459 removed outlier: 3.866A pdb=" N TYR B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.581A pdb=" N LYS B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.632A pdb=" N ALA B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.340A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER A 251 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 16 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP A 302 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 287 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.532A pdb=" N VAL A 334 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 416 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 321 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 325 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 422 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL A 327 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY A 417 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ARG A 464 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 419 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 466 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET A 421 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.713A pdb=" N GLU A 507 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 7.396A pdb=" N SER B 251 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 253 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 255 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 302 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 6.532A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 499 376 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.47: 4068 1.47 - 1.59: 5248 1.59 - 1.71: 365 1.71 - 1.84: 51 Bond restraints: 13054 Sorted by residual: bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N ILE B 385 " pdb=" CA ILE B 385 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N CYS B 50 " pdb=" CA CYS B 50 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.65e+00 bond pdb=" N LEU B 382 " pdb=" CA LEU B 382 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.42e-02 4.96e+03 6.96e+00 bond pdb=" N ARG A 438 " pdb=" CA ARG A 438 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.42e-02 4.96e+03 6.94e+00 ... (remaining 13049 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.72: 866 104.72 - 112.10: 6477 112.10 - 119.48: 4756 119.48 - 126.85: 5785 126.85 - 134.23: 571 Bond angle restraints: 18455 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 113.40 121.56 -8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" C GLU B 65 " pdb=" N ARG B 66 " pdb=" CA ARG B 66 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C4' G E 190 " pdb=" C3' G E 190 " pdb=" O3' G E 190 " ideal model delta sigma weight residual 109.40 117.19 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" C CYS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" CA TRP B 223 " pdb=" CB TRP B 223 " pdb=" CG TRP B 223 " ideal model delta sigma weight residual 113.60 122.51 -8.91 1.90e+00 2.77e-01 2.20e+01 ... (remaining 18450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 7031 35.71 - 71.42: 379 71.42 - 107.13: 17 107.13 - 142.84: 2 142.84 - 178.54: 2 Dihedral angle restraints: 7431 sinusoidal: 4364 harmonic: 3067 Sorted by residual: dihedral pdb=" O4' U E 92 " pdb=" C1' U E 92 " pdb=" N1 U E 92 " pdb=" C2 U E 92 " ideal model delta sinusoidal sigma weight residual 232.00 53.46 178.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 77 " pdb=" C1' C E 77 " pdb=" N1 C E 77 " pdb=" C2 C E 77 " ideal model delta sinusoidal sigma weight residual 232.00 56.83 175.17 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U E 110 " pdb=" C1' U E 110 " pdb=" N1 U E 110 " pdb=" C2 U E 110 " ideal model delta sinusoidal sigma weight residual -160.00 -61.24 -98.76 1 1.50e+01 4.44e-03 4.92e+01 ... (remaining 7428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1904 0.093 - 0.186: 193 0.186 - 0.279: 16 0.279 - 0.372: 5 0.372 - 0.465: 1 Chirality restraints: 2119 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C3' G E 190 " pdb=" C4' G E 190 " pdb=" O3' G E 190 " pdb=" C2' G E 190 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB THR A 389 " pdb=" CA THR A 389 " pdb=" OG1 THR A 389 " pdb=" CG2 THR A 389 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2116 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 42 " -0.031 2.00e-02 2.50e+03 2.42e-02 1.61e+01 pdb=" N9 DA C 42 " 0.064 2.00e-02 2.50e+03 pdb=" C8 DA C 42 " -0.033 2.00e-02 2.50e+03 pdb=" N7 DA C 42 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA C 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA C 42 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA C 42 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA C 42 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 197 " 0.024 2.00e-02 2.50e+03 2.31e-02 1.20e+01 pdb=" N1 U E 197 " -0.055 2.00e-02 2.50e+03 pdb=" C2 U E 197 " 0.031 2.00e-02 2.50e+03 pdb=" O2 U E 197 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U E 197 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U E 197 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C5 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U E 197 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 123 " 0.026 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 C E 123 " -0.056 2.00e-02 2.50e+03 pdb=" C2 C E 123 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C E 123 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C E 123 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C E 123 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C E 123 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C E 123 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C E 123 " 0.005 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1453 2.76 - 3.29: 10809 3.29 - 3.83: 22411 3.83 - 4.36: 27377 4.36 - 4.90: 41752 Nonbonded interactions: 103802 Sorted by model distance: nonbonded pdb=" N3 C E 22 " pdb=" N1 G E 71 " model vdw 2.220 2.600 nonbonded pdb=" OG1 THR A 9 " pdb=" O2' A E 203 " model vdw 2.282 2.440 nonbonded pdb=" N4 C E 22 " pdb=" O6 G E 71 " model vdw 2.283 2.520 nonbonded pdb=" O2 C E 87 " pdb=" O2' A E 129 " model vdw 2.291 2.440 nonbonded pdb=" O PHE B 341 " pdb=" OH TYR B 511 " model vdw 2.296 2.440 ... (remaining 103797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 525 or resid 601 through 602)) selection = chain 'B' } 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 190 5.49 5 S 37 5.16 5 C 7186 2.51 5 N 2218 2.21 5 O 2779 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 individual isotropic 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: 1.330 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: 0.020 Extract box with map and model: 4.510 Check model and map are aligned: 0.170 Process input model: 41.560 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.005 0.063 13054 Z= 0.308 Angle : 0.948 12.650 18455 Z= 0.552 Chirality : 0.059 0.465 2119 Planarity : 0.007 0.065 1666 Dihedral : 18.530 178.545 5441 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.21), residues: 1037 helix: -2.17 (0.19), residues: 444 sheet: -2.23 (0.37), residues: 167 loop : -3.07 (0.23), residues: 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.376 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3728 time to fit residues: 63.0981 Evaluate side-chains 87 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 376 HIS A 380 ASN A 493 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 13054 Z= 0.292 Angle : 0.611 8.084 18455 Z= 0.326 Chirality : 0.039 0.205 2119 Planarity : 0.004 0.051 1666 Dihedral : 17.519 173.912 3289 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.24), residues: 1037 helix: -0.39 (0.23), residues: 458 sheet: -1.53 (0.42), residues: 153 loop : -2.71 (0.26), residues: 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.136 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 113 average time/residue: 0.3252 time to fit residues: 49.6613 Evaluate side-chains 97 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1215 time to fit residues: 2.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 13054 Z= 0.363 Angle : 0.626 7.027 18455 Z= 0.335 Chirality : 0.041 0.196 2119 Planarity : 0.004 0.056 1666 Dihedral : 17.754 175.429 3289 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.25), residues: 1037 helix: 0.19 (0.24), residues: 462 sheet: -1.32 (0.42), residues: 151 loop : -2.66 (0.26), residues: 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.169 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 0.3130 time to fit residues: 49.2734 Evaluate side-chains 97 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1142 time to fit residues: 3.5826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 13054 Z= 0.322 Angle : 0.584 7.459 18455 Z= 0.312 Chirality : 0.040 0.188 2119 Planarity : 0.004 0.051 1666 Dihedral : 17.618 176.046 3289 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1037 helix: 0.54 (0.24), residues: 460 sheet: -1.21 (0.43), residues: 151 loop : -2.51 (0.27), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.222 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.3024 time to fit residues: 40.2518 Evaluate side-chains 90 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1178 time to fit residues: 3.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13054 Z= 0.196 Angle : 0.511 7.195 18455 Z= 0.273 Chirality : 0.036 0.160 2119 Planarity : 0.003 0.040 1666 Dihedral : 17.378 179.274 3289 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 1037 helix: 0.97 (0.24), residues: 460 sheet: -1.08 (0.44), residues: 150 loop : -2.36 (0.27), residues: 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.126 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 94 average time/residue: 0.3273 time to fit residues: 42.4003 Evaluate side-chains 88 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1182 time to fit residues: 2.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13054 Z= 0.207 Angle : 0.507 7.292 18455 Z= 0.271 Chirality : 0.036 0.156 2119 Planarity : 0.003 0.041 1666 Dihedral : 17.340 179.658 3289 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1037 helix: 1.16 (0.24), residues: 461 sheet: -0.78 (0.45), residues: 141 loop : -2.26 (0.27), residues: 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.236 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 100 average time/residue: 0.3181 time to fit residues: 44.2951 Evaluate side-chains 87 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1193 time to fit residues: 2.1531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 69 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13054 Z= 0.286 Angle : 0.553 8.401 18455 Z= 0.293 Chirality : 0.039 0.189 2119 Planarity : 0.004 0.043 1666 Dihedral : 17.454 177.696 3289 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1037 helix: 1.08 (0.24), residues: 460 sheet: -1.07 (0.44), residues: 149 loop : -2.25 (0.28), residues: 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.121 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 0.3061 time to fit residues: 40.4689 Evaluate side-chains 87 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1162 time to fit residues: 2.0703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 13054 Z= 0.423 Angle : 0.639 8.083 18455 Z= 0.337 Chirality : 0.043 0.214 2119 Planarity : 0.004 0.050 1666 Dihedral : 17.699 174.622 3289 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1037 helix: 0.83 (0.24), residues: 459 sheet: -1.05 (0.44), residues: 149 loop : -2.32 (0.28), residues: 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.354 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.3094 time to fit residues: 41.8870 Evaluate side-chains 90 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1141 time to fit residues: 2.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 13054 Z= 0.304 Angle : 0.575 8.208 18455 Z= 0.305 Chirality : 0.040 0.196 2119 Planarity : 0.004 0.048 1666 Dihedral : 17.541 176.740 3289 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 1037 helix: 0.93 (0.24), residues: 458 sheet: -1.05 (0.44), residues: 149 loop : -2.30 (0.28), residues: 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.105 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 0.3772 time to fit residues: 44.5804 Evaluate side-chains 82 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.0370 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13054 Z= 0.199 Angle : 0.520 8.692 18455 Z= 0.276 Chirality : 0.037 0.210 2119 Planarity : 0.004 0.045 1666 Dihedral : 17.306 179.386 3289 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1037 helix: 1.16 (0.24), residues: 461 sheet: -0.76 (0.45), residues: 139 loop : -2.25 (0.28), residues: 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.367 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.3042 time to fit residues: 36.6357 Evaluate side-chains 82 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0270 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 0.0170 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135467 restraints weight = 13659.845| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.67 r_work: 0.3260 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13054 Z= 0.152 Angle : 0.502 9.784 18455 Z= 0.268 Chirality : 0.036 0.206 2119 Planarity : 0.003 0.044 1666 Dihedral : 17.240 179.720 3289 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1037 helix: 1.29 (0.24), residues: 462 sheet: -0.68 (0.45), residues: 138 loop : -2.17 (0.28), residues: 437 =============================================================================== Job complete usr+sys time: 2205.80 seconds wall clock time: 41 minutes 47.07 seconds (2507.07 seconds total)