Starting phenix.real_space_refine on Mon Mar 11 19:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_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_25811/03_2024/7tcg_25811_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcg_25811/03_2024/7tcg_25811_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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-dev-5265/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: 5.10, per 1000 atoms: 0.57 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 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: 1.89 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: 2.47 Time building geometry restraints manager: 3.74 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: 5062 24.41 - 48.82: 355 48.82 - 73.23: 31 73.23 - 97.63: 8 97.63 - 122.04: 3 Dihedral angle restraints: 5459 sinusoidal: 2215 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 5456 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.320 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.400 Find NCS groups from input model: 0.380 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- 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 : 15.908 122.043 3373 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 % Allowed : 0.21 % Favored : 99.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.006 TRP A 605 HIS 0.002 0.000 HIS A 596 PHE 0.012 0.001 PHE A 529 TYR 0.017 0.001 TYR B 222 ARG 0.009 0.000 ARG C 122 *********************** 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 : 1.057 Fit side-chains REVERT: A 226 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7229 (mmtm) REVERT: C 134 TYR cc_start: 0.8376 (t80) cc_final: 0.8168 (t80) REVERT: C 234 THR cc_start: 0.8957 (m) cc_final: 0.8730 (t) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2127 time to fit residues: 41.2160 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9037 Z= 0.133 Angle : 0.592 24.611 12146 Z= 0.273 Chirality : 0.040 0.185 1400 Planarity : 0.003 0.038 1517 Dihedral : 8.289 107.590 1220 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.34 % Allowed : 7.63 % Favored : 91.03 % 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: -0.35 (0.26), residues: 1115 helix: 1.28 (0.23), residues: 609 sheet: -0.09 (0.76), residues: 65 loop : -2.56 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 613 HIS 0.002 0.000 HIS A 596 PHE 0.024 0.001 PHE C 82 TYR 0.018 0.001 TYR A 270 ARG 0.008 0.000 ARG C 122 *********************** 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: 13 poor density : 123 time to evaluate : 0.992 Fit side-chains REVERT: A 226 LYS cc_start: 0.7619 (ptpt) cc_final: 0.7259 (mmtm) REVERT: B 221 MET cc_start: 0.7991 (mmp) cc_final: 0.7435 (mmt) REVERT: C 134 TYR cc_start: 0.8367 (t80) cc_final: 0.8012 (t80) REVERT: C 199 MET cc_start: 0.8282 (ttm) cc_final: 0.8023 (tpp) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.1942 time to fit residues: 35.4995 Evaluate side-chains 130 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9037 Z= 0.192 Angle : 0.600 21.400 12146 Z= 0.282 Chirality : 0.041 0.166 1400 Planarity : 0.003 0.038 1517 Dihedral : 8.252 105.061 1220 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.65 % Allowed : 10.52 % Favored : 87.84 % 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: -0.38 (0.27), residues: 1115 helix: 1.27 (0.23), residues: 614 sheet: -0.45 (0.67), residues: 83 loop : -2.65 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 613 HIS 0.004 0.001 HIS A 596 PHE 0.016 0.001 PHE A 529 TYR 0.022 0.001 TYR A 270 ARG 0.005 0.000 ARG C 122 *********************** 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 136 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.123 Fit side-chains REVERT: A 132 MET cc_start: 0.8425 (mmm) cc_final: 0.8169 (tpp) REVERT: C 134 TYR cc_start: 0.8380 (t80) cc_final: 0.7991 (t80) REVERT: C 221 MET cc_start: 0.7467 (tmm) cc_final: 0.7222 (tmm) outliers start: 16 outliers final: 14 residues processed: 129 average time/residue: 0.2111 time to fit residues: 38.7479 Evaluate side-chains 132 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9037 Z= 0.162 Angle : 0.593 21.655 12146 Z= 0.275 Chirality : 0.040 0.145 1400 Planarity : 0.003 0.038 1517 Dihedral : 8.062 106.316 1220 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.65 % Allowed : 12.37 % Favored : 85.98 % 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: -0.32 (0.27), residues: 1115 helix: 1.28 (0.23), residues: 620 sheet: -0.27 (0.69), residues: 78 loop : -2.63 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 605 HIS 0.002 0.001 HIS A 596 PHE 0.027 0.001 PHE C 82 TYR 0.020 0.001 TYR A 270 ARG 0.005 0.000 ARG C 122 *********************** 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 142 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.176 Fit side-chains REVERT: A 226 LYS cc_start: 0.7669 (ptpt) cc_final: 0.7311 (mmtm) REVERT: B 221 MET cc_start: 0.8011 (mmp) cc_final: 0.7441 (mmt) REVERT: C 134 TYR cc_start: 0.8373 (t80) cc_final: 0.8076 (t80) REVERT: C 221 MET cc_start: 0.7382 (tmm) cc_final: 0.7132 (tmm) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.2059 time to fit residues: 38.7717 Evaluate side-chains 130 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9037 Z= 0.424 Angle : 0.739 22.325 12146 Z= 0.359 Chirality : 0.045 0.149 1400 Planarity : 0.004 0.038 1517 Dihedral : 8.259 108.752 1220 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.47 % Allowed : 14.33 % Favored : 83.20 % 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: -0.78 (0.26), residues: 1115 helix: 0.93 (0.23), residues: 605 sheet: -0.67 (0.66), residues: 84 loop : -2.72 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 605 HIS 0.007 0.001 HIS A 596 PHE 0.030 0.002 PHE B 236 TYR 0.024 0.002 TYR A 270 ARG 0.010 0.001 ARG C 122 *********************** 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 145 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.049 Fit side-chains REVERT: A 202 MET cc_start: 0.8050 (mmp) cc_final: 0.7369 (tpp) REVERT: A 226 LYS cc_start: 0.7668 (ptpt) cc_final: 0.7310 (mmtm) REVERT: A 580 ILE cc_start: 0.9155 (pt) cc_final: 0.8683 (mp) REVERT: B 221 MET cc_start: 0.8085 (mmp) cc_final: 0.7733 (mmt) REVERT: C 34 GLU cc_start: 0.7312 (pm20) cc_final: 0.6961 (pm20) REVERT: C 134 TYR cc_start: 0.8407 (t80) cc_final: 0.8071 (t80) REVERT: C 203 ASP cc_start: 0.8050 (p0) cc_final: 0.7807 (p0) REVERT: C 221 MET cc_start: 0.7490 (tmm) cc_final: 0.7189 (tmm) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.2004 time to fit residues: 38.4263 Evaluate side-chains 135 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0050 chunk 26 optimal weight: 0.0980 chunk 107 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9037 Z= 0.141 Angle : 0.609 21.357 12146 Z= 0.283 Chirality : 0.041 0.194 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.752 111.596 1220 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.86 % Allowed : 15.77 % Favored : 82.37 % 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: -0.46 (0.27), residues: 1115 helix: 1.15 (0.23), residues: 618 sheet: -0.37 (0.69), residues: 78 loop : -2.63 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 605 HIS 0.002 0.000 HIS B 202 PHE 0.019 0.001 PHE C 82 TYR 0.022 0.001 TYR A 270 ARG 0.008 0.000 ARG C 122 *********************** 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 137 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.084 Fit side-chains REVERT: A 226 LYS cc_start: 0.7647 (ptpt) cc_final: 0.7317 (mmtm) REVERT: B 221 MET cc_start: 0.7934 (mmp) cc_final: 0.7685 (mmt) REVERT: C 34 GLU cc_start: 0.7082 (pm20) cc_final: 0.6830 (pm20) REVERT: C 134 TYR cc_start: 0.8313 (t80) cc_final: 0.8043 (t80) REVERT: C 221 MET cc_start: 0.7230 (tmm) cc_final: 0.6989 (tmm) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.2178 time to fit residues: 40.9693 Evaluate side-chains 126 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9037 Z= 0.283 Angle : 0.669 21.520 12146 Z= 0.317 Chirality : 0.042 0.223 1400 Planarity : 0.003 0.038 1517 Dihedral : 7.601 110.229 1220 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.65 % Allowed : 16.39 % Favored : 81.96 % 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: -0.60 (0.26), residues: 1115 helix: 1.07 (0.23), residues: 614 sheet: -0.66 (0.65), residues: 84 loop : -2.69 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 605 HIS 0.005 0.001 HIS A 596 PHE 0.019 0.002 PHE A 529 TYR 0.027 0.002 TYR A 270 ARG 0.009 0.001 ARG C 122 *********************** 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 134 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.038 Fit side-chains REVERT: A 226 LYS cc_start: 0.7690 (ptpt) cc_final: 0.7299 (mmtm) REVERT: A 291 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 34 GLU cc_start: 0.7214 (pm20) cc_final: 0.6905 (pm20) REVERT: C 134 TYR cc_start: 0.8387 (t80) cc_final: 0.8182 (t80) REVERT: C 166 PHE cc_start: 0.8242 (m-80) cc_final: 0.8007 (m-80) REVERT: C 221 MET cc_start: 0.7348 (tmm) cc_final: 0.7086 (tmm) outliers start: 16 outliers final: 15 residues processed: 130 average time/residue: 0.2032 time to fit residues: 37.2325 Evaluate side-chains 130 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 99 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9037 Z= 0.165 Angle : 0.625 21.303 12146 Z= 0.290 Chirality : 0.041 0.253 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.429 108.862 1220 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.86 % Allowed : 16.80 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1115 helix: 1.20 (0.23), residues: 612 sheet: -0.43 (0.68), residues: 78 loop : -2.62 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 605 HIS 0.002 0.001 HIS A 596 PHE 0.022 0.001 PHE C 82 TYR 0.023 0.001 TYR A 270 ARG 0.010 0.000 ARG C 122 *********************** 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 136 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.058 Fit side-chains REVERT: A 226 LYS cc_start: 0.7673 (ptpt) cc_final: 0.7263 (mmtm) REVERT: B 236 PHE cc_start: 0.8567 (t80) cc_final: 0.8343 (t80) REVERT: C 34 GLU cc_start: 0.7138 (pm20) cc_final: 0.6848 (pm20) REVERT: C 134 TYR cc_start: 0.8324 (t80) cc_final: 0.8112 (t80) REVERT: C 221 MET cc_start: 0.7257 (tmm) cc_final: 0.7018 (tmm) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.2050 time to fit residues: 38.6952 Evaluate side-chains 130 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9037 Z= 0.197 Angle : 0.644 21.252 12146 Z= 0.301 Chirality : 0.042 0.251 1400 Planarity : 0.003 0.038 1517 Dihedral : 7.350 107.146 1220 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.75 % Allowed : 17.22 % Favored : 81.03 % 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: -0.55 (0.26), residues: 1115 helix: 1.12 (0.23), residues: 618 sheet: -0.64 (0.66), residues: 83 loop : -2.72 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 605 HIS 0.003 0.001 HIS A 596 PHE 0.014 0.001 PHE A 529 TYR 0.022 0.001 TYR A 270 ARG 0.009 0.000 ARG C 122 *********************** 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 134 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.119 Fit side-chains REVERT: A 226 LYS cc_start: 0.7677 (ptpt) cc_final: 0.7260 (mmtm) REVERT: B 221 MET cc_start: 0.8035 (mmp) cc_final: 0.7593 (mmt) REVERT: C 34 GLU cc_start: 0.7150 (pm20) cc_final: 0.6861 (pm20) REVERT: C 134 TYR cc_start: 0.8339 (t80) cc_final: 0.8128 (t80) REVERT: C 221 MET cc_start: 0.7299 (tmm) cc_final: 0.7042 (tmm) outliers start: 17 outliers final: 17 residues processed: 131 average time/residue: 0.1999 time to fit residues: 37.0647 Evaluate side-chains 131 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 26 optimal weight: 0.0870 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.1550 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= 0.139 Angle : 0.625 21.167 12146 Z= 0.289 Chirality : 0.040 0.245 1400 Planarity : 0.003 0.040 1517 Dihedral : 7.061 104.017 1220 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.65 % Allowed : 17.22 % Favored : 81.13 % 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: -0.29 (0.27), residues: 1115 helix: 1.37 (0.23), residues: 609 sheet: -0.42 (0.67), residues: 78 loop : -2.59 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 605 HIS 0.002 0.000 HIS A 510 PHE 0.024 0.001 PHE C 82 TYR 0.022 0.001 TYR A 270 ARG 0.009 0.000 ARG C 122 ********************** 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 138 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.065 Fit side-chains REVERT: A 226 LYS cc_start: 0.7657 (ptpt) cc_final: 0.7274 (mmtm) REVERT: B 221 MET cc_start: 0.7975 (mmp) cc_final: 0.7525 (mmt) REVERT: C 34 GLU cc_start: 0.7126 (pm20) cc_final: 0.6898 (pm20) REVERT: C 134 TYR cc_start: 0.8305 (t80) cc_final: 0.8081 (t80) REVERT: C 221 MET cc_start: 0.7162 (tmm) cc_final: 0.6946 (tmm) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.2081 time to fit residues: 39.1684 Evaluate side-chains 132 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143260 restraints weight = 11201.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142592 restraints weight = 19747.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140690 restraints weight = 19252.238| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9037 Z= 0.176 Angle : 0.638 21.215 12146 Z= 0.295 Chirality : 0.042 0.331 1400 Planarity : 0.003 0.039 1517 Dihedral : 6.933 102.553 1220 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.44 % Allowed : 18.04 % Favored : 80.52 % 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: -0.31 (0.27), residues: 1115 helix: 1.33 (0.23), residues: 613 sheet: -0.38 (0.68), residues: 78 loop : -2.61 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 605 HIS 0.002 0.000 HIS A 596 PHE 0.016 0.001 PHE A 529 TYR 0.024 0.001 TYR A 270 ARG 0.009 0.000 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.05 seconds wall clock time: 35 minutes 8.64 seconds (2108.64 seconds total)