Starting phenix.real_space_refine on Thu Sep 26 11:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj1_0009/09_2024/6gj1_0009.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.44, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 1.13 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: 2.83 Time building geometry restraints manager: 3.71 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: 0.00 - 3.23: 17222 3.23 - 6.47: 770 6.47 - 9.70: 93 9.70 - 12.94: 10 12.94 - 16.17: 8 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 Time spend for trying shortcut: 0.00 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: 0.660 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.840 Find NCS groups from input model: 0.470 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- 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 : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9404 (ttt180) cc_final: 0.9121 (ttp-110) REVERT: A 55 PHE cc_start: 0.8755 (m-10) cc_final: 0.8528 (m-10) REVERT: A 57 MET cc_start: 0.9064 (mmm) cc_final: 0.8687 (mmm) REVERT: A 194 MET cc_start: 0.7907 (tpp) cc_final: 0.7459 (tpt) REVERT: A 256 VAL cc_start: 0.8402 (t) cc_final: 0.7665 (m) REVERT: A 364 MET cc_start: 0.6897 (mtt) cc_final: 0.6534 (mtt) REVERT: A 385 MET cc_start: 0.6591 (mtt) cc_final: 0.5625 (mtt) REVERT: A 401 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8545 (mmt180) REVERT: A 465 MET cc_start: 0.8226 (mmm) cc_final: 0.7588 (mmm) REVERT: A 515 PHE cc_start: 0.8437 (t80) cc_final: 0.8151 (t80) REVERT: A 525 ASP cc_start: 0.8444 (m-30) cc_final: 0.7071 (m-30) REVERT: A 582 ASN cc_start: 0.7075 (m-40) cc_final: 0.6472 (m-40) REVERT: B 13 MET cc_start: 0.9005 (ttp) cc_final: 0.8483 (tpt) REVERT: B 55 PHE cc_start: 0.7639 (m-10) cc_final: 0.7357 (m-80) REVERT: B 80 TRP cc_start: 0.8098 (t-100) cc_final: 0.7315 (t-100) REVERT: B 321 TYR cc_start: 0.9315 (p90) cc_final: 0.9009 (p90) REVERT: B 397 TRP cc_start: 0.7166 (t-100) cc_final: 0.6946 (t-100) REVERT: B 402 MET cc_start: 0.8375 (mmm) cc_final: 0.8045 (tpp) REVERT: B 474 ASN cc_start: 0.8500 (m-40) cc_final: 0.8231 (t0) REVERT: B 551 PHE cc_start: 0.8511 (m-10) cc_final: 0.7702 (m-80) REVERT: B 565 THR cc_start: 0.7144 (t) cc_final: 0.6843 (t) REVERT: B 577 TRP cc_start: 0.6702 (m-10) cc_final: 0.6271 (m-10) REVERT: C 14 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7957 (ttt180) REVERT: C 64 MET cc_start: 0.2043 (mtt) cc_final: 0.0857 (mmt) REVERT: C 120 ASP cc_start: 0.8858 (m-30) cc_final: 0.8415 (m-30) REVERT: C 135 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.7710 (mmt180) REVERT: C 142 TYR cc_start: 0.8588 (t80) cc_final: 0.8245 (t80) REVERT: C 242 MET cc_start: 0.8652 (pmt) cc_final: 0.8348 (pmm) REVERT: C 250 ASN cc_start: 0.8780 (m-40) cc_final: 0.8238 (m110) REVERT: D 40 ILE cc_start: 0.7716 (pt) cc_final: 0.7365 (pt) REVERT: D 48 LEU cc_start: 0.7797 (tt) cc_final: 0.7540 (mt) outliers start: 10 outliers final: 2 residues processed: 288 average time/residue: 0.3450 time to fit residues: 129.5673 Evaluate side-chains 180 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 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 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 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: 0.7209 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13327 Z= 0.303 Angle : 0.942 13.154 18103 Z= 0.487 Chirality : 0.052 0.510 1999 Planarity : 0.009 0.142 2359 Dihedral : 9.325 56.945 1829 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.58 % Favored : 84.11 % Rotamer: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 2.86 % 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: -4.79 (0.17), residues: 1630 helix: -2.77 (0.20), residues: 405 sheet: -2.38 (0.37), residues: 185 loop : -3.75 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 49 HIS 0.009 0.001 HIS B 510 PHE 0.020 0.002 PHE B 50 TYR 0.043 0.003 TYR D 84 ARG 0.025 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 : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9042 (m90) cc_final: 0.8750 (m90) REVERT: A 57 MET cc_start: 0.8915 (mmm) cc_final: 0.8565 (mmm) REVERT: A 104 MET cc_start: 0.8558 (mmt) cc_final: 0.8190 (mmm) REVERT: A 194 MET cc_start: 0.7786 (tpp) cc_final: 0.7506 (tpt) REVERT: A 256 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.7959 (m) REVERT: A 364 MET cc_start: 0.6508 (mtt) cc_final: 0.6269 (mtt) REVERT: A 402 MET cc_start: 0.9203 (mtm) cc_final: 0.8672 (mtm) REVERT: A 580 ASN cc_start: 0.9039 (p0) cc_final: 0.8335 (p0) REVERT: A 582 ASN cc_start: 0.7181 (m-40) cc_final: 0.6587 (m110) REVERT: B 13 MET cc_start: 0.8990 (ttp) cc_final: 0.8308 (tpt) REVERT: B 80 TRP cc_start: 0.7717 (t-100) cc_final: 0.6917 (t-100) REVERT: B 173 LEU cc_start: 0.8852 (mt) cc_final: 0.8581 (mt) REVERT: B 230 TRP cc_start: 0.7267 (t60) cc_final: 0.6994 (t-100) REVERT: B 254 MET cc_start: 0.7860 (ttm) cc_final: 0.7521 (ttm) REVERT: B 330 ASP cc_start: 0.9566 (p0) cc_final: 0.9294 (t0) REVERT: B 397 TRP cc_start: 0.7017 (t-100) cc_final: 0.6738 (t-100) REVERT: B 402 MET cc_start: 0.8260 (mmm) cc_final: 0.7205 (mmm) REVERT: B 544 PHE cc_start: 0.8481 (t80) cc_final: 0.7720 (t80) REVERT: B 546 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8735 (mt-10) REVERT: B 547 MET cc_start: 0.8551 (ptp) cc_final: 0.7787 (mtm) REVERT: B 551 PHE cc_start: 0.8369 (m-10) cc_final: 0.7316 (m-80) REVERT: C 14 ARG cc_start: 0.8310 (mtt180) cc_final: 0.8031 (tpt170) REVERT: C 58 PHE cc_start: 0.7591 (t80) cc_final: 0.6714 (t80) REVERT: C 142 TYR cc_start: 0.8363 (t80) cc_final: 0.7808 (t80) REVERT: C 153 LYS cc_start: 0.9282 (mmpt) cc_final: 0.8987 (mmmt) REVERT: C 188 LEU cc_start: 0.8829 (tp) cc_final: 0.8618 (tp) REVERT: C 250 ASN cc_start: 0.8468 (m-40) cc_final: 0.7841 (m110) outliers start: 3 outliers final: 1 residues processed: 234 average time/residue: 0.3520 time to fit residues: 108.0387 Evaluate side-chains 163 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 160 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 overall best weight: 4.3584 ------------------------------------------------------------------------------- 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 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13327 Z= 0.276 Angle : 0.878 13.586 18103 Z= 0.445 Chirality : 0.050 0.417 1999 Planarity : 0.008 0.144 2359 Dihedral : 8.634 57.153 1829 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.85 % Favored : 81.90 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.92 % 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: -4.43 (0.18), residues: 1630 helix: -2.38 (0.21), residues: 400 sheet: -2.30 (0.36), residues: 183 loop : -3.52 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 577 HIS 0.011 0.001 HIS B 510 PHE 0.027 0.002 PHE B 55 TYR 0.026 0.002 TYR C 346 ARG 0.014 0.001 ARG B 359 *********************** 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 207 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9361 (ttt180) cc_final: 0.8914 (ttp-110) REVERT: A 27 HIS cc_start: 0.8976 (m90) cc_final: 0.8766 (m-70) REVERT: A 57 MET cc_start: 0.8898 (mmm) cc_final: 0.8494 (mmm) REVERT: A 104 MET cc_start: 0.8628 (mmt) cc_final: 0.8343 (mmm) REVERT: A 194 MET cc_start: 0.7785 (tpp) cc_final: 0.7341 (tpt) REVERT: A 385 MET cc_start: 0.5435 (mtt) cc_final: 0.4450 (mtt) REVERT: A 401 ARG cc_start: 0.8826 (mtt180) cc_final: 0.8548 (mmt180) REVERT: A 402 MET cc_start: 0.9213 (mtm) cc_final: 0.8603 (mtm) REVERT: A 580 ASN cc_start: 0.8882 (p0) cc_final: 0.8045 (p0) REVERT: A 582 ASN cc_start: 0.7218 (m-40) cc_final: 0.6603 (m110) REVERT: B 13 MET cc_start: 0.9003 (ttp) cc_final: 0.8307 (tpt) REVERT: B 61 ARG cc_start: 0.8743 (mmt180) cc_final: 0.8406 (mmt180) REVERT: B 80 TRP cc_start: 0.7839 (t-100) cc_final: 0.7370 (t-100) REVERT: B 254 MET cc_start: 0.7950 (ttm) cc_final: 0.7615 (ttm) REVERT: B 359 ARG cc_start: 0.8245 (tpm170) cc_final: 0.7928 (tpm170) REVERT: B 397 TRP cc_start: 0.7052 (t-100) cc_final: 0.6821 (t-100) REVERT: B 402 MET cc_start: 0.8237 (mmm) cc_final: 0.7188 (mmm) REVERT: B 544 PHE cc_start: 0.8532 (t80) cc_final: 0.7723 (t80) REVERT: B 547 MET cc_start: 0.8559 (ptp) cc_final: 0.8224 (mtm) REVERT: C 58 PHE cc_start: 0.7554 (t80) cc_final: 0.6718 (t80) REVERT: C 64 MET cc_start: 0.1068 (mtt) cc_final: 0.0492 (mtt) REVERT: C 138 ARG cc_start: 0.8223 (tmt170) cc_final: 0.8011 (tpt90) REVERT: C 142 TYR cc_start: 0.8285 (t80) cc_final: 0.7960 (t80) REVERT: C 153 LYS cc_start: 0.9390 (mmpt) cc_final: 0.9085 (mmmt) REVERT: C 250 ASN cc_start: 0.8487 (m-40) cc_final: 0.7832 (m110) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3472 time to fit residues: 94.6871 Evaluate side-chains 153 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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: 0.0870 chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 141 optimal weight: 0.2980 chunk 42 optimal weight: 8.9990 overall best weight: 4.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 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 328 GLN C 350 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13327 Z= 0.280 Angle : 0.867 13.790 18103 Z= 0.439 Chirality : 0.049 0.350 1999 Planarity : 0.008 0.141 2359 Dihedral : 8.338 55.459 1829 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 17.30 % Favored : 82.52 % Rotamer: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.78 % 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: -4.24 (0.19), residues: 1630 helix: -2.13 (0.22), residues: 397 sheet: -2.10 (0.38), residues: 178 loop : -3.45 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 462 HIS 0.012 0.001 HIS B 510 PHE 0.034 0.002 PHE B 55 TYR 0.028 0.002 TYR C 346 ARG 0.022 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.578 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: A 27 HIS cc_start: 0.8872 (m90) cc_final: 0.8632 (m-70) REVERT: A 102 MET cc_start: 0.6662 (tpp) cc_final: 0.6374 (tpp) REVERT: A 193 MET cc_start: 0.9063 (tpt) cc_final: 0.8837 (tpp) REVERT: A 194 MET cc_start: 0.7806 (tpp) cc_final: 0.7366 (tpt) REVERT: A 321 TYR cc_start: 0.8396 (p90) cc_final: 0.8030 (p90) REVERT: A 402 MET cc_start: 0.9149 (mtm) cc_final: 0.8299 (mtm) REVERT: A 580 ASN cc_start: 0.8856 (p0) cc_final: 0.8275 (p0) REVERT: A 582 ASN cc_start: 0.7113 (m-40) cc_final: 0.6413 (m110) REVERT: B 13 MET cc_start: 0.8950 (ttp) cc_final: 0.8327 (tpp) REVERT: B 61 ARG cc_start: 0.8707 (mmt180) cc_final: 0.8463 (mmt180) REVERT: B 67 ASP cc_start: 0.8156 (p0) cc_final: 0.7910 (p0) REVERT: B 80 TRP cc_start: 0.7871 (t-100) cc_final: 0.7077 (t-100) REVERT: B 254 MET cc_start: 0.7973 (ttm) cc_final: 0.7644 (ttm) REVERT: B 359 ARG cc_start: 0.8228 (tpm170) cc_final: 0.7981 (tpm170) REVERT: B 397 TRP cc_start: 0.7041 (t-100) cc_final: 0.6837 (t-100) REVERT: B 402 MET cc_start: 0.8177 (mmm) cc_final: 0.7163 (mmm) REVERT: B 544 PHE cc_start: 0.8471 (t80) cc_final: 0.7749 (t80) REVERT: B 546 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8888 (mt-10) REVERT: B 547 MET cc_start: 0.8635 (ptp) cc_final: 0.8244 (mtp) REVERT: C 142 TYR cc_start: 0.8312 (t80) cc_final: 0.7875 (t80) REVERT: C 153 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9199 (mmmt) REVERT: C 222 LEU cc_start: 0.8532 (mt) cc_final: 0.8224 (mp) REVERT: D 66 MET cc_start: -0.1204 (tpt) cc_final: -0.1575 (tpt) REVERT: D 97 GLU cc_start: 0.7079 (pp20) cc_final: 0.6841 (pp20) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.3530 time to fit residues: 89.9463 Evaluate side-chains 147 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 82 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 172 ASN C 328 GLN D 134 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13327 Z= 0.211 Angle : 0.807 14.074 18103 Z= 0.407 Chirality : 0.048 0.383 1999 Planarity : 0.007 0.144 2359 Dihedral : 7.895 55.337 1829 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.07 % Favored : 83.74 % Rotamer: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.59 % 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: -3.94 (0.19), residues: 1630 helix: -1.74 (0.24), residues: 395 sheet: -2.09 (0.38), residues: 171 loop : -3.28 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 462 HIS 0.009 0.001 HIS B 510 PHE 0.043 0.002 PHE B 551 TYR 0.017 0.002 TYR B 240 ARG 0.011 0.001 ARG A 459 *********************** 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 195 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8685 (m90) cc_final: 0.8452 (m-70) REVERT: A 57 MET cc_start: 0.8989 (mmp) cc_final: 0.8732 (mmm) REVERT: A 78 MET cc_start: 0.8870 (mmm) cc_final: 0.8662 (mmm) REVERT: A 321 TYR cc_start: 0.8132 (p90) cc_final: 0.7773 (p90) REVERT: A 402 MET cc_start: 0.9190 (mtm) cc_final: 0.8598 (mtm) REVERT: A 542 HIS cc_start: 0.8010 (m90) cc_final: 0.7635 (m170) REVERT: A 580 ASN cc_start: 0.8919 (p0) cc_final: 0.8253 (p0) REVERT: A 582 ASN cc_start: 0.7316 (m-40) cc_final: 0.6720 (m-40) REVERT: B 13 MET cc_start: 0.8914 (ttp) cc_final: 0.8276 (tpp) REVERT: B 66 ASP cc_start: 0.9101 (t0) cc_final: 0.8898 (t0) REVERT: B 80 TRP cc_start: 0.7785 (t-100) cc_final: 0.7045 (t-100) REVERT: B 102 MET cc_start: 0.8472 (mmp) cc_final: 0.8211 (ppp) REVERT: B 170 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8821 (pp30) REVERT: B 397 TRP cc_start: 0.7000 (t-100) cc_final: 0.6776 (t-100) REVERT: B 402 MET cc_start: 0.8107 (mmm) cc_final: 0.7227 (mmm) REVERT: B 544 PHE cc_start: 0.8410 (t80) cc_final: 0.7690 (t80) REVERT: B 547 MET cc_start: 0.8454 (ptp) cc_final: 0.7721 (mtt) REVERT: B 558 MET cc_start: 0.8597 (mpp) cc_final: 0.8314 (mmp) REVERT: C 153 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9148 (mmmt) REVERT: C 192 ARG cc_start: 0.4810 (mtt-85) cc_final: 0.2331 (mtt-85) REVERT: C 222 LEU cc_start: 0.8529 (mt) cc_final: 0.8159 (mp) REVERT: D 66 MET cc_start: -0.0896 (tpt) cc_final: -0.1311 (tpt) REVERT: D 97 GLU cc_start: 0.7165 (pp20) cc_final: 0.6656 (tm-30) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.3368 time to fit residues: 87.7590 Evaluate side-chains 150 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 4.9990 chunk 141 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 53 GLN C 172 ASN C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13327 Z= 0.221 Angle : 0.800 14.392 18103 Z= 0.402 Chirality : 0.048 0.355 1999 Planarity : 0.007 0.140 2359 Dihedral : 7.654 57.270 1829 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.75 % Favored : 83.13 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % Twisted General : 0.59 % 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: -3.85 (0.19), residues: 1630 helix: -1.58 (0.24), residues: 389 sheet: -2.20 (0.37), residues: 178 loop : -3.22 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 462 HIS 0.010 0.001 HIS A 257 PHE 0.022 0.002 PHE A 55 TYR 0.016 0.002 TYR C 346 ARG 0.009 0.001 ARG B 14 *********************** 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 182 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 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: A 27 HIS cc_start: 0.8644 (m90) cc_final: 0.8421 (m-70) REVERT: A 57 MET cc_start: 0.8999 (mmp) cc_final: 0.8758 (mmm) REVERT: A 194 MET cc_start: 0.7488 (tpt) cc_final: 0.7219 (tpt) REVERT: A 321 TYR cc_start: 0.8048 (p90) cc_final: 0.7826 (p90) REVERT: A 402 MET cc_start: 0.9194 (mtm) cc_final: 0.8511 (mtm) REVERT: A 542 HIS cc_start: 0.8100 (m90) cc_final: 0.7725 (m170) REVERT: A 580 ASN cc_start: 0.8894 (p0) cc_final: 0.8265 (p0) REVERT: A 582 ASN cc_start: 0.7450 (m-40) cc_final: 0.6874 (m-40) REVERT: B 13 MET cc_start: 0.8923 (ttp) cc_final: 0.8249 (tpp) REVERT: B 80 TRP cc_start: 0.7778 (t-100) cc_final: 0.7362 (t-100) REVERT: B 102 MET cc_start: 0.8409 (mmp) cc_final: 0.8022 (ppp) REVERT: B 397 TRP cc_start: 0.6892 (t-100) cc_final: 0.6690 (t-100) REVERT: B 402 MET cc_start: 0.8022 (mmm) cc_final: 0.7150 (mmm) REVERT: B 544 PHE cc_start: 0.8449 (t80) cc_final: 0.7759 (t80) REVERT: B 546 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8908 (mt-10) REVERT: B 547 MET cc_start: 0.8418 (ptp) cc_final: 0.8024 (mtt) REVERT: B 568 VAL cc_start: 0.8136 (t) cc_final: 0.7887 (t) REVERT: C 36 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9150 (mm-30) REVERT: C 142 TYR cc_start: 0.8198 (t80) cc_final: 0.7963 (t80) REVERT: C 153 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9151 (mmmt) REVERT: C 192 ARG cc_start: 0.4848 (mtt-85) cc_final: 0.2503 (mtt-85) REVERT: C 222 LEU cc_start: 0.8622 (mt) cc_final: 0.8169 (mp) REVERT: D 66 MET cc_start: -0.1265 (tpt) cc_final: -0.1655 (tpt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3281 time to fit residues: 80.1249 Evaluate side-chains 148 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 157 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS C 172 ASN C 245 HIS C 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13327 Z= 0.194 Angle : 0.782 14.839 18103 Z= 0.392 Chirality : 0.048 0.354 1999 Planarity : 0.007 0.135 2359 Dihedral : 7.339 57.335 1829 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.09 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.20), residues: 1630 helix: -1.36 (0.25), residues: 384 sheet: -2.12 (0.35), residues: 192 loop : -3.17 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 168 HIS 0.006 0.001 HIS B 498 PHE 0.023 0.002 PHE B 551 TYR 0.019 0.002 TYR C 346 ARG 0.008 0.000 ARG B 359 *********************** 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: 0 poor density : 188 time to evaluate : 1.546 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: A 57 MET cc_start: 0.8970 (mmp) cc_final: 0.8705 (mmm) REVERT: A 78 MET cc_start: 0.8740 (mmp) cc_final: 0.8241 (mmm) REVERT: A 193 MET cc_start: 0.8851 (tpt) cc_final: 0.8647 (tpp) REVERT: A 194 MET cc_start: 0.7306 (tpt) cc_final: 0.6972 (tpt) REVERT: A 402 MET cc_start: 0.9201 (mtm) cc_final: 0.8564 (mtm) REVERT: A 542 HIS cc_start: 0.8074 (m90) cc_final: 0.7792 (m170) REVERT: A 543 LEU cc_start: 0.9208 (mm) cc_final: 0.8951 (pp) REVERT: A 580 ASN cc_start: 0.8850 (p0) cc_final: 0.8281 (p0) REVERT: A 582 ASN cc_start: 0.7439 (m-40) cc_final: 0.6805 (m-40) REVERT: B 13 MET cc_start: 0.8818 (ttp) cc_final: 0.8168 (tpp) REVERT: B 80 TRP cc_start: 0.7738 (t-100) cc_final: 0.6975 (t-100) REVERT: B 402 MET cc_start: 0.8011 (mmm) cc_final: 0.7051 (mmm) REVERT: B 544 PHE cc_start: 0.8332 (t80) cc_final: 0.8114 (t80) REVERT: B 547 MET cc_start: 0.8513 (ptp) cc_final: 0.7588 (ptp) REVERT: B 558 MET cc_start: 0.8552 (mpp) cc_final: 0.8254 (mmp) REVERT: C 36 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9115 (mm-30) REVERT: C 64 MET cc_start: 0.0971 (mtt) cc_final: 0.0179 (mtt) REVERT: C 142 TYR cc_start: 0.8125 (t80) cc_final: 0.7795 (t80) REVERT: C 153 LYS cc_start: 0.9397 (mmpt) cc_final: 0.9168 (mmmt) REVERT: C 192 ARG cc_start: 0.4791 (mtt-85) cc_final: 0.2401 (mtt-85) REVERT: C 222 LEU cc_start: 0.8614 (mt) cc_final: 0.8280 (mp) REVERT: D 95 MET cc_start: 0.6715 (ppp) cc_final: 0.6466 (ppp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3296 time to fit residues: 82.8392 Evaluate side-chains 149 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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: 8.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 508 GLN A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 263 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 172 ASN C 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13327 Z= 0.230 Angle : 0.798 14.658 18103 Z= 0.399 Chirality : 0.047 0.343 1999 Planarity : 0.007 0.128 2359 Dihedral : 7.239 57.402 1829 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.44 % Favored : 83.44 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.20), residues: 1630 helix: -1.37 (0.24), residues: 393 sheet: -1.88 (0.39), residues: 167 loop : -3.14 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 397 HIS 0.022 0.001 HIS A 375 PHE 0.041 0.002 PHE B 55 TYR 0.021 0.002 TYR C 346 ARG 0.013 0.001 ARG B 14 *********************** 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 174 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8939 (mmp) cc_final: 0.8649 (mmm) REVERT: A 78 MET cc_start: 0.8796 (mmp) cc_final: 0.8156 (mmm) REVERT: A 193 MET cc_start: 0.8902 (tpt) cc_final: 0.8672 (tpp) REVERT: A 194 MET cc_start: 0.7386 (tpt) cc_final: 0.7051 (tpt) REVERT: A 402 MET cc_start: 0.9208 (mtm) cc_final: 0.8468 (mtm) REVERT: A 542 HIS cc_start: 0.8113 (m90) cc_final: 0.7786 (m170) REVERT: A 580 ASN cc_start: 0.8968 (p0) cc_final: 0.8478 (p0) REVERT: A 582 ASN cc_start: 0.7826 (m-40) cc_final: 0.7208 (m-40) REVERT: B 13 MET cc_start: 0.8974 (ttp) cc_final: 0.8285 (tpp) REVERT: B 80 TRP cc_start: 0.7735 (t-100) cc_final: 0.7094 (t-100) REVERT: B 397 TRP cc_start: 0.6504 (t-100) cc_final: 0.6166 (t-100) REVERT: B 402 MET cc_start: 0.8248 (mmm) cc_final: 0.7747 (mpp) REVERT: B 547 MET cc_start: 0.8558 (ptp) cc_final: 0.7973 (ptp) REVERT: B 558 MET cc_start: 0.8698 (mpp) cc_final: 0.8463 (mmp) REVERT: C 36 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9067 (mm-30) REVERT: C 64 MET cc_start: 0.1138 (mtt) cc_final: 0.0496 (ttm) REVERT: C 142 TYR cc_start: 0.8092 (t80) cc_final: 0.7745 (t80) REVERT: C 153 LYS cc_start: 0.9440 (mmpt) cc_final: 0.9212 (mmmt) REVERT: C 192 ARG cc_start: 0.4997 (mtt-85) cc_final: 0.2624 (mtt-85) REVERT: C 222 LEU cc_start: 0.8491 (mt) cc_final: 0.8138 (mp) REVERT: D 95 MET cc_start: 0.6855 (ppp) cc_final: 0.6553 (ppp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3330 time to fit residues: 77.3047 Evaluate side-chains 141 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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: 20.0000 chunk 146 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 0.0370 chunk 145 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 172 ASN C 328 GLN D 137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13327 Z= 0.187 Angle : 0.768 14.037 18103 Z= 0.382 Chirality : 0.047 0.347 1999 Planarity : 0.007 0.124 2359 Dihedral : 6.976 55.371 1829 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.74 % Favored : 86.13 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -3.71 (0.19), residues: 1630 helix: -1.37 (0.25), residues: 398 sheet: -1.80 (0.39), residues: 172 loop : -3.24 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.012 0.001 HIS A 375 PHE 0.041 0.002 PHE B 55 TYR 0.019 0.001 TYR C 346 ARG 0.009 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 181 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8955 (mmp) cc_final: 0.8663 (mmm) REVERT: A 78 MET cc_start: 0.8716 (mmp) cc_final: 0.8273 (mmm) REVERT: A 193 MET cc_start: 0.8777 (tpt) cc_final: 0.8549 (tpp) REVERT: A 194 MET cc_start: 0.7432 (tpt) cc_final: 0.7107 (tpt) REVERT: A 402 MET cc_start: 0.9234 (mtm) cc_final: 0.8623 (mtm) REVERT: A 533 ASN cc_start: 0.7565 (t0) cc_final: 0.7315 (t0) REVERT: A 542 HIS cc_start: 0.8042 (m90) cc_final: 0.7648 (m170) REVERT: A 543 LEU cc_start: 0.9273 (mm) cc_final: 0.9027 (pp) REVERT: A 580 ASN cc_start: 0.8924 (p0) cc_final: 0.8582 (p0) REVERT: A 582 ASN cc_start: 0.7793 (m-40) cc_final: 0.7154 (m-40) REVERT: B 13 MET cc_start: 0.8922 (ttp) cc_final: 0.8123 (tpp) REVERT: B 27 HIS cc_start: 0.8862 (t70) cc_final: 0.8520 (t-90) REVERT: B 397 TRP cc_start: 0.6489 (t-100) cc_final: 0.6046 (t-100) REVERT: B 402 MET cc_start: 0.8202 (mmm) cc_final: 0.7499 (mpp) REVERT: B 547 MET cc_start: 0.8284 (ptp) cc_final: 0.7876 (ptp) REVERT: C 36 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9044 (mm-30) REVERT: C 64 MET cc_start: 0.1025 (mtt) cc_final: 0.0352 (mtt) REVERT: C 142 TYR cc_start: 0.8008 (t80) cc_final: 0.7747 (t80) REVERT: C 153 LYS cc_start: 0.9348 (mmpt) cc_final: 0.9137 (mmmt) REVERT: C 192 ARG cc_start: 0.4668 (mtt-85) cc_final: 0.2166 (mtt-85) REVERT: C 222 LEU cc_start: 0.8380 (mt) cc_final: 0.7967 (mp) REVERT: C 242 MET cc_start: 0.8400 (pmm) cc_final: 0.8187 (pmm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3224 time to fit residues: 78.5146 Evaluate side-chains 149 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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: 7.9990 chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 0.0020 chunk 129 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 99 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 172 ASN C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13327 Z= 0.212 Angle : 0.797 13.187 18103 Z= 0.394 Chirality : 0.048 0.351 1999 Planarity : 0.007 0.121 2359 Dihedral : 6.975 57.255 1829 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.09 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -3.68 (0.20), residues: 1630 helix: -1.42 (0.25), residues: 395 sheet: -1.94 (0.38), residues: 185 loop : -3.16 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 168 HIS 0.009 0.001 HIS A 375 PHE 0.041 0.002 PHE B 55 TYR 0.019 0.002 TYR C 346 ARG 0.008 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 179 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 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: A 57 MET cc_start: 0.8941 (mmp) cc_final: 0.8637 (mmm) REVERT: A 78 MET cc_start: 0.8682 (mmp) cc_final: 0.8099 (mmm) REVERT: A 193 MET cc_start: 0.8841 (tpt) cc_final: 0.8621 (tpp) REVERT: A 402 MET cc_start: 0.9238 (mtm) cc_final: 0.8559 (mtm) REVERT: A 533 ASN cc_start: 0.7563 (t0) cc_final: 0.7359 (t0) REVERT: A 542 HIS cc_start: 0.8075 (m90) cc_final: 0.7758 (m170) REVERT: A 580 ASN cc_start: 0.9034 (p0) cc_final: 0.8603 (p0) REVERT: A 582 ASN cc_start: 0.7879 (m-40) cc_final: 0.7205 (m-40) REVERT: B 13 MET cc_start: 0.8920 (ttp) cc_final: 0.8274 (tpp) REVERT: B 66 ASP cc_start: 0.9212 (t0) cc_final: 0.8996 (t0) REVERT: B 80 TRP cc_start: 0.7629 (t-100) cc_final: 0.6959 (t-100) REVERT: B 397 TRP cc_start: 0.6491 (t-100) cc_final: 0.6055 (t-100) REVERT: B 402 MET cc_start: 0.8197 (mmm) cc_final: 0.7509 (mpp) REVERT: B 543 LEU cc_start: 0.9157 (tp) cc_final: 0.8932 (tp) REVERT: B 547 MET cc_start: 0.8365 (ptp) cc_final: 0.7011 (ptp) REVERT: C 36 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9056 (mm-30) REVERT: C 64 MET cc_start: 0.1179 (mtt) cc_final: 0.0535 (ttm) REVERT: C 142 TYR cc_start: 0.8072 (t80) cc_final: 0.7781 (t80) REVERT: C 153 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9177 (mmmt) REVERT: C 192 ARG cc_start: 0.4916 (mtt-85) cc_final: 0.2353 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3304 time to fit residues: 79.2648 Evaluate side-chains 148 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 8.9990 chunk 119 optimal weight: 50.0000 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 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 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059643 restraints weight = 105838.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061076 restraints weight = 71977.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062151 restraints weight = 54255.956| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13327 Z= 0.230 Angle : 0.802 13.105 18103 Z= 0.397 Chirality : 0.048 0.356 1999 Planarity : 0.007 0.115 2359 Dihedral : 6.998 56.670 1829 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.52 % Favored : 84.36 % 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 : 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: -3.56 (0.20), residues: 1630 helix: -1.34 (0.25), residues: 385 sheet: -1.71 (0.39), residues: 173 loop : -3.09 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 168 HIS 0.009 0.001 HIS A 375 PHE 0.040 0.002 PHE B 55 TYR 0.019 0.002 TYR C 346 ARG 0.008 0.001 ARG B 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2759.90 seconds wall clock time: 49 minutes 49.65 seconds (2989.65 seconds total)