Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 22:05:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/04_2023/7v6a_31740_updated.pdb" } resolution = 3.6 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5497 2.51 5 N 1460 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2562 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2195 Unusual residues: {'5XI': 1} Classifications: {'peptide': 277, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 266, None: 1} Not linked: pdbres="GLN R 471 " pdbres="5XI R 601 " Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.22, per 1000 atoms: 0.61 Number of scatterers: 8584 At special positions: 0 Unit cell: (94.2936, 123.414, 123.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1562 8.00 N 1460 7.00 C 5497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 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: 3.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.558A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 59 removed outlier: 4.192A pdb=" N SER R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS R 58 " --> pdb=" O MET R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 93 removed outlier: 4.837A pdb=" N PHE R 70 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER R 85 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN R 87 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 91 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 4.149A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 166 through 175 Processing helix chain 'R' and resid 193 through 223 removed outlier: 4.017A pdb=" N ALA R 202 " --> pdb=" O GLY R 198 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix removed outlier: 4.386A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 412 removed outlier: 3.654A pdb=" N LEU R 406 " --> pdb=" O ILE R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 419 No H-bonds generated for 'chain 'R' and resid 416 through 419' Processing helix chain 'R' and resid 432 through 454 removed outlier: 4.299A pdb=" N CYS R 442 " --> pdb=" O GLY R 438 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR R 443 " --> pdb=" O TYR R 439 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL R 444 " --> pdb=" O TRP R 440 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 469 removed outlier: 3.742A pdb=" N PHE R 464 " --> pdb=" O PHE R 460 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG R 465 " --> pdb=" O LYS R 461 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS R 466 " --> pdb=" O LYS R 462 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU R 468 " --> pdb=" O PHE R 464 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.843A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.578A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.513A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.648A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.580A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.183A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.435A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.567A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.740A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.513A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.865A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 146 removed outlier: 3.599A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.579A pdb=" N TRP S 164 " --> pdb=" O ILE S 177 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 894 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: 2.19 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2252 1.33 - 1.45: 1739 1.45 - 1.57: 4685 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 8770 Sorted by residual: bond pdb=" C19 5XI R 601 " pdb=" N4 5XI R 601 " ideal model delta sigma weight residual 1.351 1.479 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C19 5XI R 601 " pdb=" O3 5XI R 601 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C8 5XI R 601 " pdb=" N1 5XI R 601 " ideal model delta sigma weight residual 1.439 1.480 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C9 5XI R 601 " pdb=" N2 5XI R 601 " ideal model delta sigma weight residual 1.452 1.493 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" CA THR B 181 " pdb=" CB THR B 181 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.35e-02 5.49e+03 3.35e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.66: 138 105.66 - 112.80: 4702 112.80 - 119.93: 2975 119.93 - 127.06: 4002 127.06 - 134.19: 106 Bond angle restraints: 11923 Sorted by residual: angle pdb=" N VAL R 418 " pdb=" CA VAL R 418 " pdb=" C VAL R 418 " ideal model delta sigma weight residual 112.96 108.07 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" CA TRP R 435 " pdb=" CB TRP R 435 " pdb=" CG TRP R 435 " ideal model delta sigma weight residual 113.60 119.04 -5.44 1.90e+00 2.77e-01 8.20e+00 angle pdb=" N TRP R 435 " pdb=" CA TRP R 435 " pdb=" C TRP R 435 " ideal model delta sigma weight residual 111.33 107.91 3.42 1.21e+00 6.83e-01 8.00e+00 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.38 110.13 3.25 1.23e+00 6.61e-01 6.96e+00 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 122.19 118.54 3.65 1.41e+00 5.03e-01 6.71e+00 ... (remaining 11918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4687 17.90 - 35.80: 369 35.80 - 53.70: 76 53.70 - 71.60: 11 71.60 - 89.49: 8 Dihedral angle restraints: 5151 sinusoidal: 1892 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual 93.00 136.93 -43.93 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA VAL R 434 " pdb=" C VAL R 434 " pdb=" N TRP R 435 " pdb=" CA TRP R 435 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA MET S 93 " pdb=" C MET S 93 " pdb=" N TYR S 94 " pdb=" CA TYR S 94 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1222 0.069 - 0.137: 156 0.137 - 0.206: 7 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C9 5XI R 601 " pdb=" C10 5XI R 601 " pdb=" C13 5XI R 601 " pdb=" N2 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.30 -2.65 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C14 5XI R 601 " pdb=" C15 5XI R 601 " pdb=" C18 5XI R 601 " pdb=" N3 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.62 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB ILE R 93 " pdb=" CA ILE R 93 " pdb=" CG1 ILE R 93 " pdb=" CG2 ILE R 93 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 1384 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 414 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO R 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO S 41 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 201 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE R 201 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE R 201 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA R 202 " -0.011 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 183 2.67 - 3.23: 8667 3.23 - 3.79: 13540 3.79 - 4.34: 17969 4.34 - 4.90: 29295 Nonbonded interactions: 69654 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.113 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR R 439 " pdb=" OH TYR R 443 " model vdw 2.179 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O SER B 160 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.210 2.440 ... (remaining 69649 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 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.004 0.128 8770 Z= 0.267 Angle : 0.706 7.697 11923 Z= 0.397 Chirality : 0.045 0.343 1387 Planarity : 0.004 0.056 1488 Dihedral : 13.929 89.494 3041 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 1104 helix: 0.44 (0.27), residues: 398 sheet: -2.68 (0.30), residues: 230 loop : -1.90 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2442 time to fit residues: 86.4109 Evaluate side-chains 238 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 110 ASN S 113 GLN S 174 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8770 Z= 0.223 Angle : 0.598 10.618 11923 Z= 0.312 Chirality : 0.043 0.200 1387 Planarity : 0.004 0.055 1488 Dihedral : 5.059 28.406 1226 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.81 (0.25), residues: 1104 helix: 0.37 (0.27), residues: 403 sheet: -2.28 (0.31), residues: 227 loop : -1.97 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 1.009 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 246 average time/residue: 0.2382 time to fit residues: 77.0966 Evaluate side-chains 241 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1176 time to fit residues: 3.9895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.0070 chunk 67 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 79 optimal weight: 5.9990 overall best weight: 0.1010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN S 174 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8770 Z= 0.143 Angle : 0.551 11.319 11923 Z= 0.284 Chirality : 0.041 0.165 1387 Planarity : 0.003 0.050 1488 Dihedral : 4.631 29.478 1226 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.54 (0.25), residues: 1104 helix: 0.55 (0.27), residues: 402 sheet: -2.11 (0.30), residues: 266 loop : -1.69 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 1.131 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 249 average time/residue: 0.2600 time to fit residues: 85.9254 Evaluate side-chains 235 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0955 time to fit residues: 2.5988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 266 HIS ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8770 Z= 0.238 Angle : 0.613 11.293 11923 Z= 0.311 Chirality : 0.042 0.180 1387 Planarity : 0.004 0.053 1488 Dihedral : 4.845 28.602 1226 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.46 (0.25), residues: 1104 helix: 0.52 (0.27), residues: 401 sheet: -1.90 (0.31), residues: 247 loop : -1.69 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.009 Fit side-chains outliers start: 31 outliers final: 25 residues processed: 248 average time/residue: 0.2456 time to fit residues: 79.8005 Evaluate side-chains 260 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0942 time to fit residues: 5.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8770 Z= 0.230 Angle : 0.610 11.454 11923 Z= 0.309 Chirality : 0.042 0.165 1387 Planarity : 0.004 0.055 1488 Dihedral : 4.923 29.814 1226 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.44 (0.25), residues: 1104 helix: 0.48 (0.27), residues: 400 sheet: -1.93 (0.30), residues: 272 loop : -1.53 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.092 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 242 average time/residue: 0.2442 time to fit residues: 77.9352 Evaluate side-chains 247 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0857 time to fit residues: 3.4727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0010 chunk 101 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN S 130 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.192 Angle : 0.594 11.696 11923 Z= 0.299 Chirality : 0.041 0.165 1387 Planarity : 0.003 0.054 1488 Dihedral : 4.776 29.393 1226 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.25 (0.26), residues: 1104 helix: 0.58 (0.27), residues: 399 sheet: -1.61 (0.32), residues: 259 loop : -1.55 (0.29), residues: 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 0.937 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 242 average time/residue: 0.2430 time to fit residues: 77.3295 Evaluate side-chains 244 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1072 time to fit residues: 3.7037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.0270 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8770 Z= 0.176 Angle : 0.605 11.727 11923 Z= 0.302 Chirality : 0.043 0.227 1387 Planarity : 0.003 0.053 1488 Dihedral : 4.695 28.672 1226 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.11 (0.26), residues: 1104 helix: 0.69 (0.27), residues: 394 sheet: -1.55 (0.32), residues: 259 loop : -1.42 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 1.054 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 242 average time/residue: 0.2515 time to fit residues: 79.5567 Evaluate side-chains 236 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0949 time to fit residues: 1.9473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN R 423 ASN ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.212 Angle : 0.643 11.892 11923 Z= 0.321 Chirality : 0.043 0.189 1387 Planarity : 0.004 0.053 1488 Dihedral : 4.856 29.962 1226 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1104 helix: 0.60 (0.27), residues: 399 sheet: -1.66 (0.31), residues: 275 loop : -1.40 (0.31), residues: 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 1.009 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 238 average time/residue: 0.2670 time to fit residues: 83.0920 Evaluate side-chains 246 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0873 time to fit residues: 2.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 92 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8770 Z= 0.187 Angle : 0.642 11.981 11923 Z= 0.315 Chirality : 0.043 0.182 1387 Planarity : 0.003 0.052 1488 Dihedral : 4.792 29.656 1226 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.11 (0.26), residues: 1104 helix: 0.67 (0.27), residues: 393 sheet: -1.57 (0.31), residues: 275 loop : -1.36 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 1.023 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 247 average time/residue: 0.2537 time to fit residues: 82.1347 Evaluate side-chains 246 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1450 time to fit residues: 2.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN C 11 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8770 Z= 0.220 Angle : 0.671 11.788 11923 Z= 0.331 Chirality : 0.043 0.178 1387 Planarity : 0.004 0.053 1488 Dihedral : 4.864 30.192 1226 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.10 (0.26), residues: 1104 helix: 0.64 (0.27), residues: 393 sheet: -1.41 (0.32), residues: 260 loop : -1.44 (0.30), residues: 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 239 time to evaluate : 1.041 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 240 average time/residue: 0.2552 time to fit residues: 80.1871 Evaluate side-chains 243 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0912 time to fit residues: 2.0986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132647 restraints weight = 13615.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136126 restraints weight = 6263.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138281 restraints weight = 3508.037| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8770 Z= 0.225 Angle : 0.688 11.644 11923 Z= 0.338 Chirality : 0.044 0.194 1387 Planarity : 0.004 0.053 1488 Dihedral : 4.945 31.123 1226 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.13 (0.26), residues: 1104 helix: 0.64 (0.27), residues: 391 sheet: -1.56 (0.31), residues: 278 loop : -1.35 (0.31), residues: 435 =============================================================================== Job complete usr+sys time: 2272.16 seconds wall clock time: 41 minutes 48.24 seconds (2508.24 seconds total)