Starting phenix.real_space_refine on Fri Mar 15 22:38:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/03_2024/6gj1_0009.pdb" } resolution = 4.7 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= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8271 2.51 5 N 2325 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13013 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4655 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 36, 'TRANS': 547} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4651 Classifications: {'peptide': 583} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 544} Chain: "C" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2737 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 320} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 970 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Time building chain proxies: 6.86, per 1000 atoms: 0.53 Number of scatterers: 13013 At special positions: 0 Unit cell: (129.8, 111.1, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2352 8.00 N 2325 7.00 C 8271 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: 4.87 Conformation dependent library (CDL) restraints added in 2.3 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 27.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.655A pdb=" N PHE A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.557A pdb=" N SER A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.777A pdb=" N ASP A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.034A pdb=" N GLY A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.128A pdb=" N GLU A 433 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 434 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 435 " --> pdb=" O CYS A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 458 through 471 removed outlier: 4.103A pdb=" N TRP A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 Processing helix chain 'A' and resid 487 through 493 removed outlier: 4.105A pdb=" N ARG A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.746A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 removed outlier: 4.133A pdb=" N ARG B 17 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.612A pdb=" N ALA B 32 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.807A pdb=" N GLU B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 68 removed outlier: 3.632A pdb=" N ASP B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.506A pdb=" N GLU B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.541A pdb=" N THR B 86 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.596A pdb=" N ARG B 197 " --> pdb=" O MET B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.033A pdb=" N GLU B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 458 through 469 removed outlier: 5.189A pdb=" N MET B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 537 through 553 removed outlier: 4.184A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 Processing helix chain 'C' and resid 22 through 26 removed outlier: 3.979A pdb=" N ILE C 26 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 45 through 51 removed outlier: 4.218A pdb=" N GLN C 50 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 123 through 139 removed outlier: 3.635A pdb=" N ARG C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 179 through 187 removed outlier: 4.201A pdb=" N LEU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.572A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.720A pdb=" N ASP C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 43 Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.510A pdb=" N LEU D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 85 removed outlier: 3.763A pdb=" N GLN D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 514 removed outlier: 7.895A pdb=" N THR A 565 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 526 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE A 567 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 528 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.492A pdb=" N LEU B 178 " --> pdb=" O GLY B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 305 through 307 removed outlier: 3.880A pdb=" N LEU B 307 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 412 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 411 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.858A pdb=" N GLN B 508 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 525 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 510 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AB2, first strand: chain 'C' and resid 209 through 213 Processing sheet with id=AB3, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB4, first strand: chain 'D' and resid 88 through 97 removed outlier: 4.035A pdb=" N ARG D 90 " --> pdb=" O ALA D 115 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 696 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: 2.91 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3534 1.33 - 1.45: 2992 1.45 - 1.58: 6691 1.58 - 1.70: 1 1.70 - 1.82: 109 Bond restraints: 13327 Sorted by residual: bond pdb=" CA PRO D 126 " pdb=" C PRO D 126 " ideal model delta sigma weight residual 1.522 1.466 0.055 1.16e-02 7.43e+03 2.29e+01 bond pdb=" C ASN A 582 " pdb=" N PRO A 583 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.25e-02 6.40e+03 1.88e+01 bond pdb=" C HIS C 232 " pdb=" N PRO C 233 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.88e+01 bond pdb=" ND1 HIS D 71 " pdb=" CE1 HIS D 71 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.43e+01 bond pdb=" N PRO D 126 " pdb=" CA PRO D 126 " ideal model delta sigma weight residual 1.469 1.424 0.046 1.22e-02 6.72e+03 1.41e+01 ... (remaining 13322 not shown) Histogram of bond angle deviations from ideal: 94.63 - 102.75: 112 102.75 - 110.87: 4689 110.87 - 118.99: 6206 118.99 - 127.11: 6911 127.11 - 135.23: 185 Bond angle restraints: 18103 Sorted by residual: angle pdb=" N PRO D 126 " pdb=" CA PRO D 126 " pdb=" C PRO D 126 " ideal model delta sigma weight residual 110.80 97.05 13.75 1.51e+00 4.39e-01 8.29e+01 angle pdb=" N GLY D 68 " pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 114.76 99.39 15.37 1.70e+00 3.46e-01 8.17e+01 angle pdb=" CA TYR D 84 " pdb=" CB TYR D 84 " pdb=" CG TYR D 84 " ideal model delta sigma weight residual 113.90 100.36 13.54 1.80e+00 3.09e-01 5.66e+01 angle pdb=" C ASP B 557 " pdb=" N MET B 558 " pdb=" CA MET B 558 " ideal model delta sigma weight residual 121.54 135.23 -13.69 1.91e+00 2.74e-01 5.14e+01 angle pdb=" C ARG C 345 " pdb=" N TYR C 346 " pdb=" CA TYR C 346 " ideal model delta sigma weight residual 121.54 134.89 -13.35 1.91e+00 2.74e-01 4.88e+01 ... (remaining 18098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 7378 16.03 - 32.06: 542 32.06 - 48.08: 91 48.08 - 64.11: 13 64.11 - 80.14: 6 Dihedral angle restraints: 8030 sinusoidal: 3302 harmonic: 4728 Sorted by residual: dihedral pdb=" CA ARG C 219 " pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta harmonic sigma weight residual -180.00 -112.59 -67.41 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA ILE C 220 " pdb=" C ILE C 220 " pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta harmonic sigma weight residual -180.00 -116.89 -63.11 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" N LEU A 436 " pdb=" CA LEU A 436 " ideal model delta harmonic sigma weight residual 180.00 120.74 59.26 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 8027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1806 0.113 - 0.226: 174 0.226 - 0.338: 15 0.338 - 0.451: 2 0.451 - 0.564: 2 Chirality restraints: 1999 Sorted by residual: chirality pdb=" CA THR D 43 " pdb=" N THR D 43 " pdb=" C THR D 43 " pdb=" CB THR D 43 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CA TYR D 84 " pdb=" N TYR D 84 " pdb=" C TYR D 84 " pdb=" CB TYR D 84 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 1996 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 220 " -0.086 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO C 221 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 67 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 56 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO D 57 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " -0.056 5.00e-02 4.00e+02 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 0.34 - 1.25: 19 1.25 - 2.16: 73 2.16 - 3.08: 8830 3.08 - 3.99: 33618 3.99 - 4.90: 57264 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99804 Sorted by model distance: nonbonded pdb=" N PRO A 44 " pdb=" NE ARG D 87 " model vdw 0.341 3.200 nonbonded pdb=" N PRO C 99 " pdb=" NH2 ARG D 39 " model vdw 0.378 3.200 nonbonded pdb=" CG PRO A 44 " pdb=" NH1 ARG D 87 " model vdw 0.387 3.520 nonbonded pdb=" NH1 ARG A 48 " pdb=" CB TYR D 84 " model vdw 0.529 3.520 nonbonded pdb=" CZ ARG A 48 " pdb=" CA TYR D 84 " model vdw 0.572 3.700 ... (remaining 99799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 586) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 33.610 Find NCS groups from input model: 0.650 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.010 0.106 13327 Z= 0.698 Angle : 1.510 16.172 18103 Z= 0.857 Chirality : 0.074 0.564 1999 Planarity : 0.011 0.130 2359 Dihedral : 11.649 80.140 4992 Min Nonbonded Distance : 0.341 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 18.28 % Favored : 81.35 % Rotamer: Outliers : 0.72 % Allowed : 5.30 % Favored : 93.99 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 3.81 % Twisted General : 1.57 % 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: -5.15 (0.17), residues: 1630 helix: -3.20 (0.20), residues: 381 sheet: -2.95 (0.31), residues: 231 loop : -3.84 (0.16), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP B 389 HIS 0.025 0.004 HIS B 510 PHE 0.032 0.004 PHE B 255 TYR 0.039 0.004 TYR B 240 ARG 0.024 0.002 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 280 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9404 (ttt180) cc_final: 0.9121 (ttp-110) REVERT: A 55 PHE cc_start: 0.8755 (m-10) cc_final: 0.8528 (m-10) REVERT: A 57 MET cc_start: 0.9064 (mmm) cc_final: 0.8687 (mmm) REVERT: A 194 MET cc_start: 0.7907 (tpp) cc_final: 0.7459 (tpt) REVERT: A 256 VAL cc_start: 0.8402 (t) cc_final: 0.7665 (m) REVERT: A 364 MET cc_start: 0.6897 (mtt) cc_final: 0.6534 (mtt) REVERT: A 385 MET cc_start: 0.6591 (mtt) cc_final: 0.5625 (mtt) REVERT: A 401 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8545 (mmt180) REVERT: A 465 MET cc_start: 0.8226 (mmm) cc_final: 0.7588 (mmm) REVERT: A 515 PHE cc_start: 0.8437 (t80) cc_final: 0.8151 (t80) REVERT: A 525 ASP cc_start: 0.8444 (m-30) cc_final: 0.7071 (m-30) REVERT: A 582 ASN cc_start: 0.7075 (m-40) cc_final: 0.6472 (m-40) REVERT: B 13 MET cc_start: 0.9005 (ttp) cc_final: 0.8483 (tpt) REVERT: B 55 PHE cc_start: 0.7639 (m-10) cc_final: 0.7357 (m-80) REVERT: B 80 TRP cc_start: 0.8098 (t-100) cc_final: 0.7315 (t-100) REVERT: B 321 TYR cc_start: 0.9315 (p90) cc_final: 0.9009 (p90) REVERT: B 397 TRP cc_start: 0.7166 (t-100) cc_final: 0.6946 (t-100) REVERT: B 402 MET cc_start: 0.8375 (mmm) cc_final: 0.8045 (tpp) REVERT: B 474 ASN cc_start: 0.8500 (m-40) cc_final: 0.8231 (t0) REVERT: B 551 PHE cc_start: 0.8511 (m-10) cc_final: 0.7702 (m-80) REVERT: B 565 THR cc_start: 0.7144 (t) cc_final: 0.6843 (t) REVERT: B 577 TRP cc_start: 0.6702 (m-10) cc_final: 0.6271 (m-10) REVERT: C 14 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7957 (ttt180) REVERT: C 64 MET cc_start: 0.2043 (mtt) cc_final: 0.0857 (mmt) REVERT: C 120 ASP cc_start: 0.8858 (m-30) cc_final: 0.8415 (m-30) REVERT: C 135 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.7710 (mmt180) REVERT: C 142 TYR cc_start: 0.8588 (t80) cc_final: 0.8245 (t80) REVERT: C 242 MET cc_start: 0.8652 (pmt) cc_final: 0.8348 (pmm) REVERT: C 250 ASN cc_start: 0.8780 (m-40) cc_final: 0.8238 (m110) REVERT: D 40 ILE cc_start: 0.7716 (pt) cc_final: 0.7365 (pt) REVERT: D 48 LEU cc_start: 0.7797 (tt) cc_final: 0.7540 (mt) outliers start: 10 outliers final: 2 residues processed: 288 average time/residue: 0.3527 time to fit residues: 132.6390 Evaluate side-chains 180 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 208 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 582 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 111 GLN C 127 HIS C 132 GLN C 318 GLN C 328 GLN C 350 GLN C 352 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 13327 Z= 0.319 Angle : 0.949 13.051 18103 Z= 0.490 Chirality : 0.052 0.473 1999 Planarity : 0.009 0.143 2359 Dihedral : 9.370 57.203 1829 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 16.69 % Favored : 83.01 % Rotamer: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 2.86 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.17), residues: 1630 helix: -2.79 (0.20), residues: 408 sheet: -2.42 (0.37), residues: 185 loop : -3.79 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 137 HIS 0.012 0.002 HIS B 510 PHE 0.018 0.002 PHE B 50 TYR 0.031 0.003 TYR D 84 ARG 0.048 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9214 (m90) cc_final: 0.8966 (m90) REVERT: A 57 MET cc_start: 0.8940 (mmm) cc_final: 0.8574 (mmm) REVERT: A 104 MET cc_start: 0.8500 (mmt) cc_final: 0.8157 (mmm) REVERT: A 194 MET cc_start: 0.7813 (tpp) cc_final: 0.7486 (tpt) REVERT: A 364 MET cc_start: 0.6473 (mtt) cc_final: 0.6219 (mtt) REVERT: A 385 MET cc_start: 0.6636 (mtt) cc_final: 0.5539 (mtt) REVERT: A 402 MET cc_start: 0.9193 (mtm) cc_final: 0.8509 (mpp) REVERT: A 468 LEU cc_start: 0.9409 (mt) cc_final: 0.9056 (mt) REVERT: A 580 ASN cc_start: 0.9011 (p0) cc_final: 0.8248 (p0) REVERT: A 582 ASN cc_start: 0.7213 (m-40) cc_final: 0.6545 (m-40) REVERT: B 13 MET cc_start: 0.9020 (ttp) cc_final: 0.8404 (tpt) REVERT: B 80 TRP cc_start: 0.7921 (t-100) cc_final: 0.7161 (t-100) REVERT: B 173 LEU cc_start: 0.8869 (mt) cc_final: 0.8606 (mt) REVERT: B 230 TRP cc_start: 0.7348 (t60) cc_final: 0.7101 (t-100) REVERT: B 254 MET cc_start: 0.7903 (ttm) cc_final: 0.7581 (ttm) REVERT: B 330 ASP cc_start: 0.9579 (p0) cc_final: 0.9337 (t0) REVERT: B 397 TRP cc_start: 0.7027 (t-100) cc_final: 0.6802 (t-100) REVERT: B 402 MET cc_start: 0.8214 (mmm) cc_final: 0.7125 (mmm) REVERT: B 544 PHE cc_start: 0.8522 (t80) cc_final: 0.7777 (t80) REVERT: B 546 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8663 (mt-10) REVERT: B 547 MET cc_start: 0.8614 (ptp) cc_final: 0.7802 (mtm) REVERT: B 551 PHE cc_start: 0.8413 (m-10) cc_final: 0.7326 (m-80) REVERT: B 565 THR cc_start: 0.7046 (t) cc_final: 0.6811 (t) REVERT: C 14 ARG cc_start: 0.8230 (mtt180) cc_final: 0.8020 (tpt170) REVERT: C 58 PHE cc_start: 0.7704 (t80) cc_final: 0.6845 (t80) REVERT: C 142 TYR cc_start: 0.8444 (t80) cc_final: 0.8099 (t80) REVERT: C 153 LYS cc_start: 0.9298 (mmpt) cc_final: 0.8999 (mmmt) REVERT: C 250 ASN cc_start: 0.8425 (m-40) cc_final: 0.7817 (m110) outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.3597 time to fit residues: 108.9799 Evaluate side-chains 164 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 582 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13327 Z= 0.310 Angle : 0.905 13.362 18103 Z= 0.458 Chirality : 0.050 0.479 1999 Planarity : 0.008 0.146 2359 Dihedral : 8.846 57.635 1829 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 20.18 % Favored : 79.57 % Rotamer: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.18), residues: 1630 helix: -2.43 (0.21), residues: 417 sheet: -2.51 (0.36), residues: 182 loop : -3.59 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 577 HIS 0.015 0.002 HIS A 82 PHE 0.017 0.002 PHE B 223 TYR 0.027 0.002 TYR C 346 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9376 (ttt180) cc_final: 0.9000 (ttp-110) REVERT: A 104 MET cc_start: 0.8604 (mmt) cc_final: 0.8356 (mmm) REVERT: A 321 TYR cc_start: 0.8296 (p90) cc_final: 0.8057 (p90) REVERT: A 401 ARG cc_start: 0.8850 (mtt180) cc_final: 0.8554 (mmt180) REVERT: A 402 MET cc_start: 0.9152 (mtm) cc_final: 0.8533 (mtm) REVERT: A 580 ASN cc_start: 0.8883 (p0) cc_final: 0.8140 (p0) REVERT: A 582 ASN cc_start: 0.7229 (m110) cc_final: 0.6480 (m110) REVERT: B 13 MET cc_start: 0.8993 (ttp) cc_final: 0.8300 (tpt) REVERT: B 80 TRP cc_start: 0.7991 (t-100) cc_final: 0.7208 (t-100) REVERT: B 102 MET cc_start: 0.8847 (mmm) cc_final: 0.8169 (ppp) REVERT: B 232 LYS cc_start: 0.8543 (mptt) cc_final: 0.8339 (mptt) REVERT: B 254 MET cc_start: 0.8065 (ttm) cc_final: 0.7721 (ttm) REVERT: B 402 MET cc_start: 0.8134 (mmm) cc_final: 0.7051 (mmm) REVERT: B 543 LEU cc_start: 0.9173 (tp) cc_final: 0.8957 (tp) REVERT: B 544 PHE cc_start: 0.8600 (t80) cc_final: 0.7738 (t80) REVERT: B 546 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8749 (mt-10) REVERT: B 547 MET cc_start: 0.8711 (ptp) cc_final: 0.8172 (mtp) REVERT: B 565 THR cc_start: 0.7111 (t) cc_final: 0.6858 (t) REVERT: C 14 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7983 (ttt180) REVERT: C 58 PHE cc_start: 0.7642 (t80) cc_final: 0.6789 (t80) REVERT: C 138 ARG cc_start: 0.8221 (tmt170) cc_final: 0.7957 (tpt90) REVERT: C 142 TYR cc_start: 0.8428 (t80) cc_final: 0.7928 (t80) REVERT: C 153 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9051 (mmmt) REVERT: C 250 ASN cc_start: 0.8332 (m-40) cc_final: 0.7653 (m110) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3506 time to fit residues: 89.8766 Evaluate side-chains 142 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 123 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13327 Z= 0.229 Angle : 0.823 13.502 18103 Z= 0.418 Chirality : 0.048 0.416 1999 Planarity : 0.007 0.145 2359 Dihedral : 8.277 58.709 1829 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.93 % Favored : 82.82 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.19), residues: 1630 helix: -2.00 (0.23), residues: 399 sheet: -1.99 (0.40), residues: 156 loop : -3.41 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 389 HIS 0.018 0.001 HIS B 467 PHE 0.038 0.002 PHE B 551 TYR 0.023 0.002 TYR C 346 ARG 0.014 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9218 (m90) cc_final: 0.9007 (m-70) REVERT: A 57 MET cc_start: 0.9027 (mmp) cc_final: 0.8814 (mmm) REVERT: A 102 MET cc_start: 0.6481 (tpp) cc_final: 0.6155 (tpp) REVERT: A 321 TYR cc_start: 0.8132 (p90) cc_final: 0.7834 (p90) REVERT: A 402 MET cc_start: 0.9172 (mtm) cc_final: 0.8564 (mtm) REVERT: A 580 ASN cc_start: 0.8818 (p0) cc_final: 0.8289 (p0) REVERT: A 582 ASN cc_start: 0.7225 (m110) cc_final: 0.6478 (m110) REVERT: B 13 MET cc_start: 0.8985 (ttp) cc_final: 0.8398 (tpt) REVERT: B 66 ASP cc_start: 0.8931 (t0) cc_final: 0.8727 (t0) REVERT: B 80 TRP cc_start: 0.7832 (t-100) cc_final: 0.7416 (t-100) REVERT: B 254 MET cc_start: 0.7996 (ttm) cc_final: 0.7664 (ttm) REVERT: B 397 TRP cc_start: 0.6983 (t-100) cc_final: 0.6649 (t-100) REVERT: B 402 MET cc_start: 0.8281 (mmm) cc_final: 0.7763 (mpp) REVERT: B 467 HIS cc_start: 0.8053 (t70) cc_final: 0.7717 (t-90) REVERT: B 544 PHE cc_start: 0.8549 (t80) cc_final: 0.7789 (t80) REVERT: B 547 MET cc_start: 0.8501 (ptp) cc_final: 0.7885 (mtt) REVERT: B 551 PHE cc_start: 0.8395 (m-80) cc_final: 0.8159 (m-80) REVERT: C 58 PHE cc_start: 0.7591 (t80) cc_final: 0.6752 (t80) REVERT: C 91 MET cc_start: 0.4966 (ptp) cc_final: 0.3545 (mmp) REVERT: C 142 TYR cc_start: 0.8380 (t80) cc_final: 0.7962 (t80) REVERT: C 153 LYS cc_start: 0.9455 (mmpt) cc_final: 0.9117 (mmmt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3673 time to fit residues: 94.3403 Evaluate side-chains 146 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS B 27 HIS B 82 HIS B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13327 Z= 0.186 Angle : 0.792 13.746 18103 Z= 0.397 Chirality : 0.048 0.379 1999 Planarity : 0.007 0.143 2359 Dihedral : 7.698 58.802 1829 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.26 % Favored : 83.56 % Rotamer: Outliers : 0.21 % Allowed : 3.58 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.20), residues: 1630 helix: -1.61 (0.25), residues: 387 sheet: -2.18 (0.37), residues: 181 loop : -3.30 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 577 HIS 0.008 0.001 HIS B 510 PHE 0.026 0.002 PHE B 551 TYR 0.026 0.002 TYR B 555 ARG 0.006 0.000 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9072 (m90) cc_final: 0.8826 (m-70) REVERT: A 364 MET cc_start: 0.7792 (tmm) cc_final: 0.7172 (ttp) REVERT: A 402 MET cc_start: 0.9201 (mtm) cc_final: 0.8549 (mtm) REVERT: A 543 LEU cc_start: 0.9305 (mm) cc_final: 0.9047 (pp) REVERT: A 580 ASN cc_start: 0.8868 (p0) cc_final: 0.8279 (p0) REVERT: A 582 ASN cc_start: 0.7428 (m110) cc_final: 0.6763 (m110) REVERT: B 13 MET cc_start: 0.8841 (ttp) cc_final: 0.8041 (tpp) REVERT: B 80 TRP cc_start: 0.7673 (t-100) cc_final: 0.6944 (t-100) REVERT: B 254 MET cc_start: 0.7827 (ttm) cc_final: 0.7488 (ttm) REVERT: B 397 TRP cc_start: 0.6899 (t-100) cc_final: 0.6471 (t-100) REVERT: B 402 MET cc_start: 0.8217 (mmm) cc_final: 0.7526 (mpp) REVERT: B 544 PHE cc_start: 0.8346 (t80) cc_final: 0.7405 (t80) REVERT: B 547 MET cc_start: 0.8512 (ptp) cc_final: 0.7872 (mtt) REVERT: C 14 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7924 (ttt180) REVERT: C 91 MET cc_start: 0.4921 (ptp) cc_final: 0.3436 (mmt) REVERT: C 142 TYR cc_start: 0.8298 (t80) cc_final: 0.7805 (t80) REVERT: C 153 LYS cc_start: 0.9423 (mmpt) cc_final: 0.9156 (mmmt) REVERT: C 164 LEU cc_start: 0.8823 (mt) cc_final: 0.8538 (mt) REVERT: C 179 ARG cc_start: 0.8399 (mpp-170) cc_final: 0.8034 (mpt-90) REVERT: C 184 LEU cc_start: 0.9648 (tt) cc_final: 0.9293 (tp) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.3600 time to fit residues: 97.5055 Evaluate side-chains 153 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 174 HIS B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 581 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 103 HIS C 328 GLN D 134 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13327 Z= 0.194 Angle : 0.785 15.030 18103 Z= 0.391 Chirality : 0.047 0.337 1999 Planarity : 0.007 0.136 2359 Dihedral : 7.485 58.912 1829 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.32 % Favored : 83.56 % Rotamer: Outliers : 0.14 % Allowed : 2.86 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.20), residues: 1630 helix: -1.51 (0.24), residues: 393 sheet: -2.06 (0.37), residues: 175 loop : -3.25 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 230 HIS 0.009 0.001 HIS C 283 PHE 0.037 0.002 PHE B 55 TYR 0.026 0.002 TYR A 321 ARG 0.005 0.001 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9005 (m90) cc_final: 0.8750 (m90) REVERT: A 57 MET cc_start: 0.8972 (mmp) cc_final: 0.8720 (mmm) REVERT: A 385 MET cc_start: 0.4533 (ttm) cc_final: 0.4288 (ttm) REVERT: A 402 MET cc_start: 0.9191 (mtm) cc_final: 0.8508 (mtm) REVERT: A 580 ASN cc_start: 0.8860 (p0) cc_final: 0.8259 (p0) REVERT: A 582 ASN cc_start: 0.7687 (m110) cc_final: 0.7013 (m-40) REVERT: B 13 MET cc_start: 0.8863 (ttp) cc_final: 0.7973 (tpp) REVERT: B 61 ARG cc_start: 0.8597 (mmt180) cc_final: 0.8375 (mmt90) REVERT: B 80 TRP cc_start: 0.7711 (t-100) cc_final: 0.7237 (t-100) REVERT: B 254 MET cc_start: 0.7713 (ttm) cc_final: 0.7305 (ttm) REVERT: B 544 PHE cc_start: 0.8406 (t80) cc_final: 0.7559 (t80) REVERT: C 36 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9100 (mm-30) REVERT: C 91 MET cc_start: 0.4865 (ptp) cc_final: 0.3430 (mmt) REVERT: C 142 TYR cc_start: 0.8248 (t80) cc_final: 0.7829 (t80) REVERT: C 153 LYS cc_start: 0.9465 (mmpt) cc_final: 0.9193 (mmmt) REVERT: C 192 ARG cc_start: 0.5078 (mtt-85) cc_final: 0.2460 (mtt-85) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.3314 time to fit residues: 81.7057 Evaluate side-chains 142 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 328 GLN C 350 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13327 Z= 0.336 Angle : 0.904 14.831 18103 Z= 0.453 Chirality : 0.051 0.387 1999 Planarity : 0.008 0.133 2359 Dihedral : 7.833 58.788 1829 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 31.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 20.12 % Favored : 79.75 % Rotamer: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.19), residues: 1630 helix: -1.70 (0.23), residues: 389 sheet: -2.44 (0.34), residues: 210 loop : -3.21 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 397 HIS 0.017 0.002 HIS A 82 PHE 0.043 0.003 PHE B 551 TYR 0.029 0.002 TYR B 555 ARG 0.008 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9008 (m90) cc_final: 0.8635 (m90) REVERT: A 57 MET cc_start: 0.9044 (mmp) cc_final: 0.8802 (mmm) REVERT: A 78 MET cc_start: 0.8767 (mmp) cc_final: 0.8259 (mmm) REVERT: A 102 MET cc_start: 0.6224 (tpp) cc_final: 0.5994 (tpp) REVERT: A 402 MET cc_start: 0.9148 (mtm) cc_final: 0.8362 (mtm) REVERT: A 580 ASN cc_start: 0.9196 (p0) cc_final: 0.8758 (p0) REVERT: A 582 ASN cc_start: 0.7810 (m110) cc_final: 0.7124 (m-40) REVERT: B 13 MET cc_start: 0.8792 (ttp) cc_final: 0.7935 (tpp) REVERT: B 80 TRP cc_start: 0.7855 (t-100) cc_final: 0.7163 (t-100) REVERT: B 254 MET cc_start: 0.7888 (ttm) cc_final: 0.7667 (ttm) REVERT: B 397 TRP cc_start: 0.6744 (t-100) cc_final: 0.6240 (t-100) REVERT: B 544 PHE cc_start: 0.8136 (t80) cc_final: 0.7606 (t80) REVERT: B 547 MET cc_start: 0.7910 (mtm) cc_final: 0.6764 (mtm) REVERT: C 36 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9197 (mm-30) REVERT: C 64 MET cc_start: 0.1438 (mtt) cc_final: 0.0863 (mtt) REVERT: C 91 MET cc_start: 0.4482 (ptp) cc_final: 0.3028 (mmt) REVERT: C 135 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8444 (mmt-90) REVERT: C 153 LYS cc_start: 0.9496 (mmpt) cc_final: 0.9211 (mmmt) REVERT: C 192 ARG cc_start: 0.5166 (mtt-85) cc_final: 0.2674 (mtt-85) REVERT: C 222 LEU cc_start: 0.8528 (mt) cc_final: 0.8250 (mp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.3197 time to fit residues: 75.2021 Evaluate side-chains 130 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13327 Z= 0.242 Angle : 0.828 14.843 18103 Z= 0.414 Chirality : 0.048 0.338 1999 Planarity : 0.007 0.133 2359 Dihedral : 7.625 59.248 1829 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.48 % Favored : 82.39 % Rotamer: Outliers : 0.07 % Allowed : 1.29 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.19), residues: 1630 helix: -1.65 (0.23), residues: 398 sheet: -2.43 (0.34), residues: 214 loop : -3.23 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 397 HIS 0.008 0.001 HIS C 283 PHE 0.034 0.002 PHE A 55 TYR 0.022 0.002 TYR B 555 ARG 0.020 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8969 (m90) cc_final: 0.8582 (m90) REVERT: A 57 MET cc_start: 0.9000 (mmp) cc_final: 0.8384 (mmm) REVERT: A 78 MET cc_start: 0.8637 (mmp) cc_final: 0.8188 (mmm) REVERT: A 402 MET cc_start: 0.9108 (mtm) cc_final: 0.8528 (mtm) REVERT: A 580 ASN cc_start: 0.9151 (p0) cc_final: 0.8707 (p0) REVERT: A 582 ASN cc_start: 0.7730 (m110) cc_final: 0.7047 (m110) REVERT: B 13 MET cc_start: 0.8765 (ttp) cc_final: 0.7865 (tpp) REVERT: B 78 MET cc_start: 0.8193 (mmp) cc_final: 0.7985 (mmt) REVERT: B 80 TRP cc_start: 0.7690 (t-100) cc_final: 0.7073 (t-100) REVERT: B 102 MET cc_start: 0.8693 (tpp) cc_final: 0.7552 (ppp) REVERT: B 254 MET cc_start: 0.7543 (ttm) cc_final: 0.7304 (ttm) REVERT: B 321 TYR cc_start: 0.9149 (p90) cc_final: 0.8874 (p90) REVERT: B 397 TRP cc_start: 0.6793 (t-100) cc_final: 0.6207 (t-100) REVERT: B 402 MET cc_start: 0.8473 (tmm) cc_final: 0.8055 (tmm) REVERT: B 519 PHE cc_start: 0.8251 (m-80) cc_final: 0.7832 (m-80) REVERT: B 544 PHE cc_start: 0.8020 (t80) cc_final: 0.7407 (t80) REVERT: B 547 MET cc_start: 0.7931 (mtm) cc_final: 0.7617 (mtm) REVERT: C 42 GLN cc_start: 0.8957 (tt0) cc_final: 0.8641 (tm-30) REVERT: C 58 PHE cc_start: 0.8304 (m-80) cc_final: 0.8012 (t80) REVERT: C 64 MET cc_start: 0.1275 (mtt) cc_final: 0.0774 (mtt) REVERT: C 91 MET cc_start: 0.4305 (ptp) cc_final: 0.2806 (mmt) REVERT: C 135 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8327 (mmt-90) REVERT: C 142 TYR cc_start: 0.8548 (t80) cc_final: 0.8235 (t80) REVERT: C 153 LYS cc_start: 0.9451 (mmpt) cc_final: 0.9128 (mmmt) REVERT: C 192 ARG cc_start: 0.4896 (mtt-85) cc_final: 0.2463 (mtt-85) REVERT: C 222 LEU cc_start: 0.8672 (mt) cc_final: 0.8310 (mp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.3420 time to fit residues: 80.9832 Evaluate side-chains 138 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 172 ASN C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13327 Z= 0.223 Angle : 0.816 14.654 18103 Z= 0.403 Chirality : 0.048 0.346 1999 Planarity : 0.007 0.129 2359 Dihedral : 7.429 59.444 1829 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 18.28 % Favored : 81.60 % Rotamer: Outliers : 0.14 % Allowed : 1.07 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.20), residues: 1630 helix: -1.53 (0.24), residues: 395 sheet: -2.34 (0.34), residues: 214 loop : -3.24 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 168 HIS 0.008 0.001 HIS B 467 PHE 0.037 0.002 PHE B 55 TYR 0.022 0.002 TYR B 555 ARG 0.010 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8944 (m90) cc_final: 0.8552 (m90) REVERT: A 57 MET cc_start: 0.8989 (mmp) cc_final: 0.8706 (mmm) REVERT: A 78 MET cc_start: 0.8455 (mmp) cc_final: 0.7956 (mmm) REVERT: A 402 MET cc_start: 0.9104 (mtm) cc_final: 0.8520 (mtm) REVERT: A 580 ASN cc_start: 0.9185 (p0) cc_final: 0.8711 (p0) REVERT: A 582 ASN cc_start: 0.7774 (m110) cc_final: 0.7047 (m110) REVERT: B 13 MET cc_start: 0.8866 (ttp) cc_final: 0.7809 (tpp) REVERT: B 78 MET cc_start: 0.8150 (mmp) cc_final: 0.7931 (mmt) REVERT: B 80 TRP cc_start: 0.7661 (t-100) cc_final: 0.7096 (t-100) REVERT: B 254 MET cc_start: 0.7521 (ttm) cc_final: 0.7267 (ttm) REVERT: B 321 TYR cc_start: 0.9107 (p90) cc_final: 0.8806 (p90) REVERT: B 519 PHE cc_start: 0.8244 (m-80) cc_final: 0.7814 (m-80) REVERT: B 544 PHE cc_start: 0.7889 (t80) cc_final: 0.7535 (t80) REVERT: B 546 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8881 (mt-10) REVERT: C 42 GLN cc_start: 0.8918 (tt0) cc_final: 0.8617 (tm-30) REVERT: C 58 PHE cc_start: 0.8375 (m-80) cc_final: 0.8068 (t80) REVERT: C 64 MET cc_start: 0.1353 (mtt) cc_final: 0.0793 (mtt) REVERT: C 91 MET cc_start: 0.4382 (ptp) cc_final: 0.2888 (mmt) REVERT: C 142 TYR cc_start: 0.8504 (t80) cc_final: 0.7922 (t80) REVERT: C 153 LYS cc_start: 0.9461 (mmpt) cc_final: 0.9159 (mmmt) REVERT: C 192 ARG cc_start: 0.4941 (mtt-85) cc_final: 0.2536 (mtt-85) REVERT: C 222 LEU cc_start: 0.8725 (mt) cc_final: 0.8443 (mp) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.3469 time to fit residues: 81.4167 Evaluate side-chains 135 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 40.0000 chunk 129 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13327 Z= 0.252 Angle : 0.833 14.615 18103 Z= 0.413 Chirality : 0.049 0.410 1999 Planarity : 0.007 0.129 2359 Dihedral : 7.461 60.078 1829 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 19.14 % Favored : 80.80 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.20), residues: 1630 helix: -1.59 (0.24), residues: 401 sheet: -2.28 (0.35), residues: 214 loop : -3.29 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 168 HIS 0.009 0.001 HIS A 82 PHE 0.041 0.002 PHE B 551 TYR 0.026 0.002 TYR B 555 ARG 0.008 0.001 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8973 (m90) cc_final: 0.8522 (m90) REVERT: A 50 PHE cc_start: 0.9012 (m-80) cc_final: 0.8774 (m-80) REVERT: A 57 MET cc_start: 0.8995 (mmp) cc_final: 0.8712 (mmm) REVERT: A 402 MET cc_start: 0.9089 (mtm) cc_final: 0.8519 (mtm) REVERT: A 580 ASN cc_start: 0.9199 (p0) cc_final: 0.8701 (p0) REVERT: A 582 ASN cc_start: 0.8086 (m110) cc_final: 0.7335 (m110) REVERT: B 13 MET cc_start: 0.8891 (ttp) cc_final: 0.8172 (tpp) REVERT: B 80 TRP cc_start: 0.7794 (t-100) cc_final: 0.7151 (t-100) REVERT: B 230 TRP cc_start: 0.7225 (t-100) cc_final: 0.6793 (t-100) REVERT: B 254 MET cc_start: 0.7574 (ttm) cc_final: 0.7285 (ttm) REVERT: B 321 TYR cc_start: 0.9134 (p90) cc_final: 0.8859 (p90) REVERT: B 359 ARG cc_start: 0.7648 (tpm170) cc_final: 0.7093 (tpm170) REVERT: B 397 TRP cc_start: 0.6468 (t-100) cc_final: 0.5904 (t-100) REVERT: B 402 MET cc_start: 0.8576 (tmm) cc_final: 0.7957 (tmm) REVERT: B 519 PHE cc_start: 0.8322 (m-80) cc_final: 0.7847 (m-80) REVERT: B 544 PHE cc_start: 0.8019 (t80) cc_final: 0.7371 (t80) REVERT: B 546 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8855 (mt-10) REVERT: B 547 MET cc_start: 0.7904 (mtm) cc_final: 0.7503 (mtm) REVERT: C 42 GLN cc_start: 0.8930 (tt0) cc_final: 0.8638 (tm-30) REVERT: C 64 MET cc_start: 0.1646 (mtt) cc_final: 0.1004 (mtt) REVERT: C 91 MET cc_start: 0.4467 (ptp) cc_final: 0.2985 (mmt) REVERT: C 142 TYR cc_start: 0.8498 (t80) cc_final: 0.7885 (t80) REVERT: C 153 LYS cc_start: 0.9469 (mmpt) cc_final: 0.9158 (mmmt) REVERT: C 192 ARG cc_start: 0.4983 (mtt-85) cc_final: 0.2581 (mtt-85) REVERT: C 222 LEU cc_start: 0.8748 (mt) cc_final: 0.8466 (mp) REVERT: D 66 MET cc_start: -0.1282 (tpt) cc_final: -0.1543 (tpt) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.3315 time to fit residues: 76.3619 Evaluate side-chains 141 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS B 416 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 172 ASN C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.073263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056078 restraints weight = 107893.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057303 restraints weight = 76863.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058251 restraints weight = 59852.064| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13327 Z= 0.260 Angle : 0.837 14.131 18103 Z= 0.415 Chirality : 0.049 0.391 1999 Planarity : 0.007 0.127 2359 Dihedral : 7.431 60.600 1829 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 19.26 % Favored : 80.67 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.19), residues: 1630 helix: -1.70 (0.23), residues: 412 sheet: -2.26 (0.35), residues: 217 loop : -3.32 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 168 HIS 0.010 0.001 HIS C 283 PHE 0.035 0.002 PHE B 551 TYR 0.026 0.002 TYR B 555 ARG 0.008 0.001 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.90 seconds wall clock time: 50 minutes 45.86 seconds (3045.86 seconds total)