Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:47:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/04_2023/7tcg_25811_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5763 2.51 5 N 1465 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" 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: 8891 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5002 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'I0O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.23, per 1000 atoms: 0.59 Number of scatterers: 8891 At special positions: 0 Unit cell: (87.2, 88.072, 158.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1623 8.00 N 1465 7.00 C 5763 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: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 52.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 3.704A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 40 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.797A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 4.352A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 3.936A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 removed outlier: 4.120A pdb=" N LYS A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 3.571A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.094A pdb=" N ILE A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.675A pdb=" N SER A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 4.238A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N MET A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 324 removed outlier: 3.649A pdb=" N SER A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 4.152A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.792A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.636A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 513 through 555 removed outlier: 3.576A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 566 removed outlier: 5.369A pdb=" N ILE A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 4.199A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 615 through 643 removed outlier: 4.040A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 102 through 110 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.062A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.690A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 102 through 113 Proline residue: C 109 - end of helix removed outlier: 4.275A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.544A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.431A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.766A pdb=" N VAL A 363 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 403 through 405 removed outlier: 7.155A pdb=" N PHE A 405 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 440 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= D, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.510A pdb=" N TYR B 13 " --> pdb=" O GLN B 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.501A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.503A pdb=" N HIS C 65 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 36 through 38 removed outlier: 6.007A pdb=" N ARG C 212 " --> pdb=" O SER C 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 375 hydrogen bonds defined for protein. 1113 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: 2.39 Time building geometry restraints manager: 3.76 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: 2794 1.34 - 1.46: 1603 1.46 - 1.58: 4564 1.58 - 1.70: 2 1.70 - 1.82: 74 Bond restraints: 9037 Sorted by residual: bond pdb=" C23 I0O A 701 " pdb=" C25 I0O A 701 " ideal model delta sigma weight residual 1.602 1.504 0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C25 I0O A 701 " pdb=" C26 I0O A 701 " ideal model delta sigma weight residual 1.589 1.515 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C18 I0O A 701 " pdb=" C20 I0O A 701 " ideal model delta sigma weight residual 1.576 1.502 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C26 I0O A 701 " pdb=" C27 I0O A 701 " ideal model delta sigma weight residual 1.566 1.498 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C21 I0O A 701 " pdb=" C22 I0O A 701 " ideal model delta sigma weight residual 1.564 1.498 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 9032 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.30: 99 105.30 - 112.46: 4615 112.46 - 119.62: 2993 119.62 - 126.78: 4389 126.78 - 133.94: 50 Bond angle restraints: 12146 Sorted by residual: angle pdb=" C44 I0O A 701 " pdb=" C43 I0O A 701 " pdb=" C45 I0O A 701 " ideal model delta sigma weight residual 68.19 115.07 -46.88 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C19 I0O A 701 " pdb=" C18 I0O A 701 " pdb=" C20 I0O A 701 " ideal model delta sigma weight residual 68.21 114.91 -46.70 3.00e+00 1.11e-01 2.42e+02 angle pdb=" C24 I0O A 701 " pdb=" C23 I0O A 701 " pdb=" C25 I0O A 701 " ideal model delta sigma weight residual 74.54 115.37 -40.83 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C17 I0O A 701 " pdb=" C18 I0O A 701 " pdb=" C19 I0O A 701 " ideal model delta sigma weight residual 85.83 123.47 -37.64 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C42 I0O A 701 " pdb=" C43 I0O A 701 " pdb=" C45 I0O A 701 " ideal model delta sigma weight residual 85.85 121.32 -35.47 3.00e+00 1.11e-01 1.40e+02 ... (remaining 12141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 5061 24.41 - 48.82: 354 48.82 - 73.23: 30 73.23 - 97.63: 8 97.63 - 122.04: 2 Dihedral angle restraints: 5455 sinusoidal: 2211 harmonic: 3244 Sorted by residual: dihedral pdb=" CA ASP C 218 " pdb=" C ASP C 218 " pdb=" N GLY C 219 " pdb=" CA GLY C 219 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLY A 609 " pdb=" C GLY A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER A 610 " pdb=" C SER A 610 " pdb=" N GLU A 611 " pdb=" CA GLU A 611 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1160 0.053 - 0.106: 210 0.106 - 0.160: 27 0.160 - 0.213: 2 0.213 - 0.266: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB ILE C 197 " pdb=" CA ILE C 197 " pdb=" CG1 ILE C 197 " pdb=" CG2 ILE C 197 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C9 I0O A 701 " pdb=" C10 I0O A 701 " pdb=" C8 I0O A 701 " pdb=" N16 I0O A 701 " both_signs ideal model delta sigma weight residual False -2.58 -2.37 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 164 " pdb=" CA ILE C 164 " pdb=" CG1 ILE C 164 " pdb=" CG2 ILE C 164 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1397 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 I0O A 701 " 0.062 2.00e-02 2.50e+03 5.24e-02 3.43e+01 pdb=" C32 I0O A 701 " -0.084 2.00e-02 2.50e+03 pdb=" C33 I0O A 701 " -0.020 2.00e-02 2.50e+03 pdb=" C34 I0O A 701 " -0.007 2.00e-02 2.50e+03 pdb=" C35 I0O A 701 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 I0O A 701 " 0.048 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" C27 I0O A 701 " -0.066 2.00e-02 2.50e+03 pdb=" C28 I0O A 701 " -0.006 2.00e-02 2.50e+03 pdb=" C29 I0O A 701 " 0.035 2.00e-02 2.50e+03 pdb=" C30 I0O A 701 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 I0O A 701 " -0.057 2.00e-02 2.50e+03 3.71e-02 1.72e+01 pdb=" C12 I0O A 701 " -0.018 2.00e-02 2.50e+03 pdb=" C14 I0O A 701 " -0.005 2.00e-02 2.50e+03 pdb=" C15 I0O A 701 " 0.036 2.00e-02 2.50e+03 pdb=" C5 I0O A 701 " 0.044 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 133 2.69 - 3.24: 8597 3.24 - 3.80: 12819 3.80 - 4.35: 16037 4.35 - 4.90: 27148 Nonbonded interactions: 64734 Sorted by model distance: nonbonded pdb=" OG1 THR B 101 " pdb=" OE1 GLU B 104 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.170 2.440 nonbonded pdb=" ND2 ASN A 362 " pdb=" OD1 ASN A 382 " model vdw 2.220 2.520 nonbonded pdb=" OG SER C 145 " pdb=" OE1 GLN C 148 " model vdw 2.266 2.440 nonbonded pdb=" ND2 ASN A 14 " pdb=" OE2 GLU A 107 " model vdw 2.322 2.520 ... (remaining 64729 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 'B' selection = chain 'C' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.690 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.670 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.098 9037 Z= 0.283 Angle : 1.153 46.880 12146 Z= 0.441 Chirality : 0.042 0.266 1400 Planarity : 0.004 0.063 1517 Dihedral : 15.715 122.043 3369 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -0.53 (0.27), residues: 1115 helix: 1.10 (0.23), residues: 606 sheet: -0.34 (0.72), residues: 72 loop : -2.57 (0.27), residues: 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2040 time to fit residues: 39.8594 Evaluate side-chains 120 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9037 Z= 0.134 Angle : 0.590 24.642 12146 Z= 0.273 Chirality : 0.040 0.185 1400 Planarity : 0.003 0.038 1517 Dihedral : 7.831 106.931 1216 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 1.13 % 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: -0.36 (0.26), residues: 1115 helix: 1.26 (0.23), residues: 609 sheet: -0.08 (0.76), residues: 65 loop : -2.55 (0.27), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.033 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 131 average time/residue: 0.2011 time to fit residues: 37.6466 Evaluate side-chains 132 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0916 time to fit residues: 3.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9037 Z= 0.195 Angle : 0.601 21.249 12146 Z= 0.283 Chirality : 0.041 0.164 1400 Planarity : 0.003 0.038 1517 Dihedral : 7.581 101.638 1216 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 1115 helix: 1.24 (0.23), residues: 615 sheet: -0.44 (0.67), residues: 83 loop : -2.66 (0.27), residues: 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.054 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 126 average time/residue: 0.2109 time to fit residues: 38.0818 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0809 time to fit residues: 1.9377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9037 Z= 0.283 Angle : 0.647 21.307 12146 Z= 0.309 Chirality : 0.042 0.165 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.605 102.571 1216 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.82 % 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: -0.55 (0.27), residues: 1115 helix: 1.10 (0.23), residues: 615 sheet: -0.55 (0.66), residues: 83 loop : -2.67 (0.27), residues: 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.076 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.2065 time to fit residues: 38.2501 Evaluate side-chains 125 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0903 time to fit residues: 2.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9037 Z= 0.288 Angle : 0.653 21.315 12146 Z= 0.314 Chirality : 0.042 0.198 1400 Planarity : 0.003 0.054 1517 Dihedral : 7.625 102.718 1216 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.93 % 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: -0.68 (0.26), residues: 1115 helix: 0.96 (0.22), residues: 621 sheet: -0.69 (0.65), residues: 84 loop : -2.71 (0.27), residues: 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.106 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.2081 time to fit residues: 38.0960 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0888 time to fit residues: 2.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 9037 Z= 0.151 Angle : 0.606 21.469 12146 Z= 0.283 Chirality : 0.040 0.176 1400 Planarity : 0.003 0.045 1517 Dihedral : 7.484 101.685 1216 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.52 % 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: -0.45 (0.26), residues: 1115 helix: 1.19 (0.23), residues: 619 sheet: -0.50 (0.68), residues: 78 loop : -2.66 (0.27), residues: 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.046 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.2000 time to fit residues: 35.9893 Evaluate side-chains 120 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0838 time to fit residues: 1.9806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9037 Z= 0.271 Angle : 0.653 21.398 12146 Z= 0.311 Chirality : 0.042 0.144 1400 Planarity : 0.003 0.044 1517 Dihedral : 7.488 100.790 1216 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 1.03 % 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: -0.57 (0.27), residues: 1115 helix: 1.11 (0.23), residues: 615 sheet: -0.75 (0.65), residues: 84 loop : -2.70 (0.27), residues: 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.978 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 119 average time/residue: 0.2128 time to fit residues: 36.0193 Evaluate side-chains 117 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1016 time to fit residues: 2.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9037 Z= 0.155 Angle : 0.611 21.466 12146 Z= 0.286 Chirality : 0.040 0.143 1400 Planarity : 0.003 0.041 1517 Dihedral : 7.357 99.493 1216 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.52 % 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: -0.43 (0.26), residues: 1115 helix: 1.19 (0.23), residues: 619 sheet: -0.45 (0.67), residues: 78 loop : -2.64 (0.27), residues: 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.017 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 122 average time/residue: 0.2011 time to fit residues: 35.1148 Evaluate side-chains 120 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0932 time to fit residues: 2.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9037 Z= 0.153 Angle : 0.616 21.479 12146 Z= 0.285 Chirality : 0.040 0.209 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.249 97.957 1216 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % 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: -0.33 (0.27), residues: 1115 helix: 1.31 (0.23), residues: 613 sheet: -0.53 (0.67), residues: 78 loop : -2.59 (0.27), residues: 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.123 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2181 time to fit residues: 36.5761 Evaluate side-chains 117 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0770 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 26 optimal weight: 0.0060 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9037 Z= 0.145 Angle : 0.621 21.492 12146 Z= 0.288 Chirality : 0.040 0.179 1400 Planarity : 0.003 0.039 1517 Dihedral : 7.178 96.752 1216 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.10 % 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: -0.28 (0.27), residues: 1115 helix: 1.38 (0.23), residues: 613 sheet: -0.53 (0.67), residues: 78 loop : -2.60 (0.27), residues: 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.023 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.2112 time to fit residues: 37.6020 Evaluate side-chains 119 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0848 time to fit residues: 1.6804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 24 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.200450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.162508 restraints weight = 11108.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.161915 restraints weight = 25946.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158607 restraints weight = 12494.744| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 9037 Z= 0.143 Angle : 0.629 21.511 12146 Z= 0.291 Chirality : 0.040 0.182 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.062 94.650 1216 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.31 % 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: -0.18 (0.27), residues: 1115 helix: 1.44 (0.23), residues: 613 sheet: -0.54 (0.69), residues: 71 loop : -2.47 (0.27), residues: 431 =============================================================================== Job complete usr+sys time: 1836.95 seconds wall clock time: 34 minutes 16.93 seconds (2056.93 seconds total)