Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:23:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/02_2023/6gj1_0009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/02_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_0009/02_2023/6gj1_0009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/02_2023/6gj1_0009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/02_2023/6gj1_0009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/02_2023/6gj1_0009.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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-4877/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: 7.35, per 1000 atoms: 0.56 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: 4.90 Conformation dependent library (CDL) restraints added in 1.9 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: 0.52 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: 3.14 Time building geometry restraints manager: 5.33 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 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. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 3.110 Check model and map are aligned: 0.210 Process input model: 33.330 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 1.509 16.172 18103 Z= 0.856 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 % 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 *********************** 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 : 1.641 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: 0.3550 time to fit residues: 133.7084 Evaluate side-chains 170 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4024 time to fit residues: 3.1897 ------------------------------------------------------------------------------- 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 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 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 13327 Z= 0.279 Angle : 0.919 13.318 18103 Z= 0.473 Chirality : 0.051 0.521 1999 Planarity : 0.009 0.141 2359 Dihedral : 9.221 56.249 1829 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 16.01 % Favored : 83.68 % Rotamer Outliers : 0.29 % 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: -4.77 (0.18), residues: 1630 helix: -2.74 (0.20), residues: 406 sheet: -2.38 (0.37), residues: 185 loop : -3.74 (0.17), residues: 1039 *********************** 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 236 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.563 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 outliers start: 4 outliers final: 1 residues processed: 236 average time/residue: 0.3514 time to fit residues: 109.0501 Evaluate side-chains 153 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1120 time to fit residues: 2.1477 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 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 33 GLN C 250 ASN C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 13327 Z= 0.346 Angle : 0.935 13.277 18103 Z= 0.472 Chirality : 0.051 0.397 1999 Planarity : 0.008 0.146 2359 Dihedral : 8.862 58.355 1829 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 30.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 20.06 % Favored : 79.69 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.98 % 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: -4.48 (0.18), residues: 1630 helix: -2.41 (0.22), residues: 402 sheet: -2.49 (0.36), residues: 182 loop : -3.52 (0.17), residues: 1046 *********************** 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 190 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.587 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 outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.3568 time to fit residues: 89.8782 Evaluate side-chains 137 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1188 time to fit residues: 2.3628 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 70 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 chunk 42 optimal weight: 30.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 416 ASN B 467 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 328 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13327 Z= 0.191 Angle : 0.812 14.161 18103 Z= 0.407 Chirality : 0.048 0.388 1999 Planarity : 0.007 0.141 2359 Dihedral : 7.880 57.358 1829 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.54 % Favored : 85.28 % Rotamer Outliers : 0.07 % 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: -4.07 (0.19), residues: 1630 helix: -1.91 (0.24), residues: 398 sheet: -2.08 (0.37), residues: 175 loop : -3.35 (0.18), residues: 1057 *********************** 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 208 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.622 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: 1 outliers final: 0 residues processed: 208 average time/residue: 0.3523 time to fit residues: 97.4352 Evaluate side-chains 151 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9314 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS B 27 HIS B 174 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 37 GLN C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13327 Z= 0.204 Angle : 0.797 14.259 18103 Z= 0.399 Chirality : 0.047 0.371 1999 Planarity : 0.007 0.138 2359 Dihedral : 7.616 56.929 1829 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.56 % Favored : 83.31 % Rotamer Outliers : 0.07 % 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: -3.93 (0.19), residues: 1630 helix: -1.71 (0.25), residues: 389 sheet: -2.16 (0.36), residues: 189 loop : -3.27 (0.18), residues: 1052 *********************** 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 192 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.687 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 outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.3609 time to fit residues: 92.3687 Evaluate side-chains 144 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3019 ------------------------------------------------------------------------------- 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: 0.0470 chunk 141 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 27 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** B 542 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN D 134 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.5803 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= 0.192 Angle : 0.783 14.849 18103 Z= 0.389 Chirality : 0.047 0.392 1999 Planarity : 0.007 0.139 2359 Dihedral : 7.343 57.039 1829 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.64 % Favored : 84.23 % Rotamer Outliers : 0.07 % 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: -3.79 (0.20), residues: 1630 helix: -1.53 (0.25), residues: 385 sheet: -2.08 (0.36), residues: 189 loop : -3.19 (0.18), residues: 1056 *********************** 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 190 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.517 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: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3577 time to fit residues: 90.7246 Evaluate side-chains 141 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1996 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 0.0470 chunk 97 optimal weight: 8.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 360 HIS B 27 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13327 Z= 0.191 Angle : 0.787 14.883 18103 Z= 0.386 Chirality : 0.047 0.362 1999 Planarity : 0.007 0.131 2359 Dihedral : 7.181 58.412 1829 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.07 % Favored : 83.80 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % 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: -3.76 (0.20), residues: 1630 helix: -1.42 (0.25), residues: 393 sheet: -2.09 (0.35), residues: 197 loop : -3.22 (0.19), residues: 1040 *********************** 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 188 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.694 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: 188 average time/residue: 0.3659 time to fit residues: 91.5051 Evaluate side-chains 143 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0918 ------------------------------------------------------------------------------- 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: 0.0570 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 123 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS B 170 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 13327 Z= 0.198 Angle : 0.776 14.146 18103 Z= 0.383 Chirality : 0.047 0.302 1999 Planarity : 0.007 0.118 2359 Dihedral : 7.036 56.986 1829 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.40 % Favored : 84.48 % Rotamer Outliers : 0.14 % 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: -3.65 (0.20), residues: 1630 helix: -1.41 (0.26), residues: 384 sheet: -1.99 (0.36), residues: 193 loop : -3.10 (0.19), residues: 1053 *********************** 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 182 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.512 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: 2 outliers final: 0 residues processed: 182 average time/residue: 0.3410 time to fit residues: 83.7298 Evaluate side-chains 146 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1494 ------------------------------------------------------------------------------- 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: 10.0000 chunk 146 optimal weight: 0.1980 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 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 C 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6461 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= 0.244 Angle : 0.813 14.378 18103 Z= 0.402 Chirality : 0.048 0.317 1999 Planarity : 0.007 0.115 2359 Dihedral : 7.156 58.243 1829 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.30 % Favored : 82.58 % Rotamer Outliers : 0.07 % 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: -3.63 (0.20), residues: 1630 helix: -1.41 (0.26), residues: 385 sheet: -1.83 (0.39), residues: 179 loop : -3.11 (0.18), residues: 1066 *********************** 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: 1 poor density : 175 time to evaluate : 1.542 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 outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3785 time to fit residues: 90.3780 Evaluate side-chains 133 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0778 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 444 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 13327 Z= 0.226 Angle : 0.810 13.381 18103 Z= 0.400 Chirality : 0.048 0.297 1999 Planarity : 0.007 0.114 2359 Dihedral : 7.083 57.799 1829 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.20 % Favored : 83.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % 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: -3.71 (0.20), residues: 1630 helix: -1.55 (0.25), residues: 392 sheet: -1.78 (0.39), residues: 179 loop : -3.16 (0.18), residues: 1059 ********************** 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: 0 poor density : 172 time to evaluate : 1.432 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 outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3256 time to fit residues: 77.1965 Evaluate side-chains 131 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1042 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 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 33 GLN C 37 GLN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.076160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059268 restraints weight = 106070.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060506 restraints weight = 76437.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.061335 restraints weight = 59950.811| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 13327 Z= 0.200 Angle : 0.795 13.216 18103 Z= 0.390 Chirality : 0.047 0.291 1999 Planarity : 0.007 0.110 2359 Dihedral : 6.961 56.588 1829 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.07 % Favored : 83.80 % Rotamer Outliers : 0.00 % 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: -3.64 (0.20), residues: 1630 helix: -1.43 (0.25), residues: 391 sheet: -1.76 (0.39), residues: 181 loop : -3.14 (0.18), residues: 1058 =============================================================================== Job complete usr+sys time: 2750.16 seconds wall clock time: 50 minutes 33.35 seconds (3033.35 seconds total)