Starting phenix.real_space_refine on Sun Dec 10 01:36:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/12_2023/6gj1_0009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/12_2023/6gj1_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_0009/12_2023/6gj1_0009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/12_2023/6gj1_0009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/12_2023/6gj1_0009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/12_2023/6gj1_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-1.21rc1-5172/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: 6.90, 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: 5.03 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: 1.22 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: 2.97 Time building geometry restraints manager: 5.50 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: 0.520 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: 2.490 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.810 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- 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 : 1.792 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 outliers start: 10 outliers final: 2 residues processed: 288 average time/residue: 0.3764 time to fit residues: 141.5196 Evaluate side-chains 170 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4014 time to fit residues: 2.8336 ------------------------------------------------------------------------------- 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: 3.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 127 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 208 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 103 HIS C 111 GLN C 127 HIS C 132 GLN C 250 ASN C 318 GLN C 328 GLN C 350 GLN C 352 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 13327 Z= 0.286 Angle : 0.915 13.380 18103 Z= 0.473 Chirality : 0.051 0.505 1999 Planarity : 0.009 0.141 2359 Dihedral : 9.200 56.348 1829 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 16.01 % Favored : 83.68 % Rotamer: Outliers : 0.21 % Allowed : 4.37 % Favored : 95.42 % 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: -4.76 (0.18), residues: 1630 helix: -2.72 (0.20), residues: 406 sheet: -2.39 (0.37), residues: 185 loop : -3.73 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 49 HIS 0.010 0.001 HIS B 510 PHE 0.029 0.002 PHE B 55 TYR 0.028 0.002 TYR D 84 ARG 0.041 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 235 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 1.503 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 outliers start: 3 outliers final: 1 residues processed: 235 average time/residue: 0.3538 time to fit residues: 109.3081 Evaluate side-chains 157 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1142 time to fit residues: 2.2869 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 0.0870 chunk 132 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- 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** B 542 HIS B 582 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 250 ASN C 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4269 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= 0.339 Angle : 0.924 13.306 18103 Z= 0.469 Chirality : 0.050 0.384 1999 Planarity : 0.008 0.146 2359 Dihedral : 8.843 58.333 1829 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.88 % Favored : 79.88 % Rotamer: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % 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: -4.45 (0.18), residues: 1630 helix: -2.34 (0.22), residues: 398 sheet: -2.48 (0.36), residues: 182 loop : -3.52 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 49 HIS 0.017 0.002 HIS A 82 PHE 0.028 0.002 PHE B 55 TYR 0.027 0.002 TYR C 346 ARG 0.010 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 : 1.538 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 outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.3499 time to fit residues: 90.4227 Evaluate side-chains 139 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1397 time to fit residues: 2.5866 ------------------------------------------------------------------------------- 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: 8.9990 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 533 ASN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 82 HIS ** 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** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4807 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= 0.198 Angle : 0.808 13.696 18103 Z= 0.408 Chirality : 0.048 0.403 1999 Planarity : 0.007 0.143 2359 Dihedral : 8.113 58.175 1829 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.07 % Favored : 83.74 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.72 % 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: -4.06 (0.19), residues: 1630 helix: -1.98 (0.24), residues: 385 sheet: -1.98 (0.39), residues: 161 loop : -3.32 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 577 HIS 0.008 0.001 HIS B 510 PHE 0.022 0.002 PHE C 58 TYR 0.021 0.002 TYR C 346 ARG 0.007 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 194 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.635 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 outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3548 time to fit residues: 91.9891 Evaluate side-chains 146 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0317 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 170 GLN ** 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 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 37 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 350 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13327 Z= 0.280 Angle : 0.845 13.265 18103 Z= 0.426 Chirality : 0.049 0.422 1999 Planarity : 0.008 0.147 2359 Dihedral : 8.027 60.328 1829 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 19.33 % Favored : 80.49 % Rotamer: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.13 % 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: -4.02 (0.19), residues: 1630 helix: -1.78 (0.24), residues: 376 sheet: -2.35 (0.35), residues: 203 loop : -3.29 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 462 HIS 0.013 0.002 HIS A 82 PHE 0.024 0.002 PHE B 55 TYR 0.025 0.002 TYR C 346 ARG 0.013 0.001 ARG A 550 *********************** 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 182 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.612 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 outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3453 time to fit residues: 84.0923 Evaluate side-chains 139 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1054 ------------------------------------------------------------------------------- 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: 10.0000 chunk 141 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 174 HIS ** 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** B 581 HIS C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13327 Z= 0.263 Angle : 0.845 14.114 18103 Z= 0.425 Chirality : 0.049 0.433 1999 Planarity : 0.007 0.143 2359 Dihedral : 7.968 60.836 1829 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 18.96 % Favored : 80.86 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: -3.98 (0.19), residues: 1630 helix: -1.81 (0.24), residues: 385 sheet: -2.35 (0.36), residues: 191 loop : -3.23 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 462 HIS 0.012 0.001 HIS B 510 PHE 0.035 0.002 PHE B 55 TYR 0.016 0.002 TYR A 374 ARG 0.012 0.001 ARG A 550 *********************** 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 179 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.535 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 outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3571 time to fit residues: 85.8999 Evaluate side-chains 134 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2263 ------------------------------------------------------------------------------- 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: 20.0000 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 0.0670 chunk 115 optimal weight: 9.9990 chunk 132 optimal weight: 0.1980 chunk 88 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** 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 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13327 Z= 0.235 Angle : 0.838 14.764 18103 Z= 0.415 Chirality : 0.049 0.380 1999 Planarity : 0.007 0.134 2359 Dihedral : 7.708 57.848 1829 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 18.83 % Favored : 81.04 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -3.93 (0.20), residues: 1630 helix: -1.75 (0.24), residues: 394 sheet: -2.29 (0.35), residues: 195 loop : -3.22 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 577 HIS 0.009 0.001 HIS B 510 PHE 0.036 0.002 PHE B 55 TYR 0.016 0.002 TYR B 555 ARG 0.010 0.001 ARG C 112 *********************** 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 178 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.414 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 outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3472 time to fit residues: 82.5950 Evaluate side-chains 135 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0469 ------------------------------------------------------------------------------- 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: 9.9990 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 170 GLN ** 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 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13327 Z= 0.289 Angle : 0.872 14.858 18103 Z= 0.435 Chirality : 0.050 0.358 1999 Planarity : 0.007 0.138 2359 Dihedral : 7.761 59.410 1829 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 20.18 % Favored : 79.69 % Rotamer: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.35 % 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: -4.01 (0.19), residues: 1630 helix: -1.87 (0.23), residues: 399 sheet: -2.28 (0.35), residues: 207 loop : -3.27 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 577 HIS 0.012 0.001 HIS A 82 PHE 0.028 0.002 PHE A 55 TYR 0.020 0.002 TYR C 346 ARG 0.009 0.001 ARG C 163 *********************** 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 169 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.564 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 outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.3511 time to fit residues: 79.5818 Evaluate side-chains 132 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9517 ------------------------------------------------------------------------------- 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: 0.8980 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 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 172 ASN C 283 HIS C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.6293 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= 0.191 Angle : 0.824 15.112 18103 Z= 0.406 Chirality : 0.048 0.307 1999 Planarity : 0.007 0.131 2359 Dihedral : 7.276 57.158 1829 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.89 % Favored : 83.99 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: -3.90 (0.19), residues: 1630 helix: -1.58 (0.24), residues: 411 sheet: -2.12 (0.36), residues: 194 loop : -3.33 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 577 HIS 0.005 0.001 HIS C 283 PHE 0.027 0.002 PHE B 55 TYR 0.017 0.002 TYR C 346 ARG 0.014 0.001 ARG B 14 *********************** 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 186 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.628 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 outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3600 time to fit residues: 90.6891 Evaluate side-chains 146 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0966 ------------------------------------------------------------------------------- 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: 9.9990 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 107 optimal weight: 8.9990 chunk 162 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 79 optimal weight: 0.0470 chunk 102 optimal weight: 4.9990 overall best weight: 3.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 172 ASN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13327 Z= 0.236 Angle : 0.840 16.968 18103 Z= 0.412 Chirality : 0.048 0.320 1999 Planarity : 0.007 0.132 2359 Dihedral : 7.241 59.518 1829 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 18.22 % Favored : 81.66 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % 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: -1.57 (0.24), residues: 406 sheet: -2.04 (0.37), residues: 194 loop : -3.30 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 577 HIS 0.009 0.001 HIS A 257 PHE 0.033 0.002 PHE B 551 TYR 0.019 0.002 TYR C 346 ARG 0.009 0.001 ARG B 14 ********************** 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 174 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.728 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 outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3729 time to fit residues: 87.0909 Evaluate side-chains 139 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2939 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS ** A 562 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 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 172 ASN C 245 HIS C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.075850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060490 restraints weight = 109384.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061890 restraints weight = 74933.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062915 restraints weight = 56466.444| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13327 Z= 0.202 Angle : 0.811 14.177 18103 Z= 0.399 Chirality : 0.048 0.307 1999 Planarity : 0.007 0.129 2359 Dihedral : 7.150 58.544 1829 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.44 % Favored : 83.44 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -3.83 (0.20), residues: 1630 helix: -1.52 (0.24), residues: 409 sheet: -1.88 (0.37), residues: 194 loop : -3.32 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 577 HIS 0.006 0.001 HIS B 467 PHE 0.035 0.002 PHE B 55 TYR 0.018 0.001 TYR C 346 ARG 0.010 0.001 ARG B 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.73 seconds wall clock time: 52 minutes 51.08 seconds (3171.08 seconds total)