Starting phenix.real_space_refine on Thu Sep 18 01:33:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_0009.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_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 { model { file = "/net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_0009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_0009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_0009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gj1_0009/09_2025/6gj1_0009.map" } 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.11, per 1000 atoms: 0.24 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 413.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 1.81 Time building geometry restraints manager: 1.76 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: 15 1.25 - 2.16: 68 2.16 - 3.08: 8830 3.08 - 3.99: 33618 3.99 - 4.90: 57264 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99795 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=" CZ ARG A 48 " pdb=" CA TYR D 84 " model vdw 0.572 2.960 nonbonded pdb=" OE2 GLU D 26 " pdb=" CD1 LEU D 131 " model vdw 0.762 3.460 ... (remaining 99790 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- 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 : 0.014 0.901 13329 Z= 1.071 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.024 0.002 ARG B 550 TYR 0.039 0.004 TYR B 240 PHE 0.032 0.004 PHE B 255 TRP 0.034 0.005 TRP B 389 HIS 0.025 0.004 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.01032 (13327) covalent geometry : angle 1.50971 (18103) hydrogen bonds : bond 0.23923 ( 262) hydrogen bonds : angle 8.63152 ( 696) Misc. bond : bond 0.73815 ( 2) *********************** 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 to be fit. rotamer outliers: 10 poor density : 280 time to evaluate : 0.530 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: A 14 ARG cc_start: 0.9404 (ttt180) cc_final: 0.9120 (ttp-110) REVERT: A 55 PHE cc_start: 0.8755 (m-10) cc_final: 0.8523 (m-10) REVERT: A 57 MET cc_start: 0.9064 (mmm) cc_final: 0.8688 (mmm) REVERT: A 194 MET cc_start: 0.7907 (tpp) cc_final: 0.7462 (tpt) REVERT: A 256 VAL cc_start: 0.8402 (t) cc_final: 0.7663 (m) REVERT: A 364 MET cc_start: 0.6897 (mtt) cc_final: 0.6534 (mtt) REVERT: A 401 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8542 (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: 0.8147 (t80) REVERT: A 525 ASP cc_start: 0.8444 (m-30) cc_final: 0.7033 (m-30) REVERT: A 582 ASN cc_start: 0.7075 (m-40) cc_final: 0.6460 (m-40) REVERT: B 13 MET cc_start: 0.9005 (ttp) cc_final: 0.8481 (tpt) REVERT: B 55 PHE cc_start: 0.7639 (m-10) cc_final: 0.7352 (m-80) REVERT: B 80 TRP cc_start: 0.8098 (t-100) cc_final: 0.7316 (t-100) REVERT: B 321 TYR cc_start: 0.9315 (p90) cc_final: 0.9010 (p90) REVERT: B 397 TRP cc_start: 0.7166 (t-100) cc_final: 0.6941 (t-100) REVERT: B 402 MET cc_start: 0.8375 (mmm) cc_final: 0.8044 (tpp) REVERT: B 474 ASN cc_start: 0.8500 (m-40) cc_final: 0.8228 (t0) REVERT: B 480 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6950 (mp0) REVERT: B 551 PHE cc_start: 0.8511 (m-10) cc_final: 0.7703 (m-80) REVERT: B 565 THR cc_start: 0.7144 (t) cc_final: 0.6851 (t) REVERT: B 577 TRP cc_start: 0.6702 (m-10) cc_final: 0.6258 (m-10) REVERT: C 14 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7959 (ttt180) REVERT: C 64 MET cc_start: 0.2043 (mtt) cc_final: 0.0806 (mmt) REVERT: C 120 ASP cc_start: 0.8858 (m-30) cc_final: 0.8414 (m-30) REVERT: C 135 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.7712 (mmt180) REVERT: C 142 TYR cc_start: 0.8588 (t80) cc_final: 0.8229 (t80) REVERT: C 242 MET cc_start: 0.8652 (pmt) cc_final: 0.8352 (pmm) REVERT: C 250 ASN cc_start: 0.8780 (m-40) cc_final: 0.8236 (m110) REVERT: D 40 ILE cc_start: 0.7716 (pt) cc_final: 0.7364 (pt) REVERT: D 48 LEU cc_start: 0.7797 (tt) cc_final: 0.7541 (mt) outliers start: 10 outliers final: 2 residues processed: 288 average time/residue: 0.1641 time to fit residues: 61.3829 Evaluate side-chains 182 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 111 GLN C 127 HIS C 132 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 328 GLN C 350 GLN C 352 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.075003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059529 restraints weight = 104032.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060991 restraints weight = 70254.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062074 restraints weight = 52306.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062892 restraints weight = 41743.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063509 restraints weight = 34814.409| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 13329 Z= 0.230 Angle : 0.952 13.056 18103 Z= 0.495 Chirality : 0.052 0.570 1999 Planarity : 0.009 0.142 2359 Dihedral : 9.373 57.057 1829 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.89 % Favored : 83.93 % Rotamer: Outliers : 0.21 % Allowed : 4.44 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 2.86 % Twisted General : 1.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.81 (0.18), residues: 1630 helix: -2.78 (0.20), residues: 410 sheet: -2.42 (0.37), residues: 185 loop : -3.76 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 324 TYR 0.028 0.003 TYR C 346 PHE 0.022 0.002 PHE B 50 TRP 0.037 0.003 TRP C 49 HIS 0.010 0.002 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00468 (13327) covalent geometry : angle 0.95229 (18103) hydrogen bonds : bond 0.05648 ( 262) hydrogen bonds : angle 6.88582 ( 696) Misc. bond : bond 0.01961 ( 2) *********************** 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 234 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.9087 (m90) cc_final: 0.8737 (m90) REVERT: A 57 MET cc_start: 0.9072 (mmm) cc_final: 0.8686 (mmm) REVERT: A 104 MET cc_start: 0.8812 (mmt) cc_final: 0.8533 (mmm) REVERT: A 194 MET cc_start: 0.7900 (tpp) cc_final: 0.7644 (tpt) REVERT: A 256 VAL cc_start: 0.8653 (t) cc_final: 0.8060 (m) REVERT: A 364 MET cc_start: 0.6849 (mtt) cc_final: 0.6295 (mtt) REVERT: A 402 MET cc_start: 0.9212 (mtm) cc_final: 0.8653 (mtm) REVERT: A 468 LEU cc_start: 0.9400 (mt) cc_final: 0.9043 (mt) REVERT: A 580 ASN cc_start: 0.9064 (p0) cc_final: 0.8367 (p0) REVERT: A 582 ASN cc_start: 0.7424 (m-40) cc_final: 0.6801 (m110) REVERT: B 13 MET cc_start: 0.9009 (ttp) cc_final: 0.8330 (tpt) REVERT: B 27 HIS cc_start: 0.9056 (t70) cc_final: 0.8830 (t70) REVERT: B 55 PHE cc_start: 0.7617 (m-10) cc_final: 0.7376 (m-80) REVERT: B 80 TRP cc_start: 0.8017 (t-100) cc_final: 0.7152 (t-100) REVERT: B 173 LEU cc_start: 0.8939 (mt) cc_final: 0.8629 (mt) REVERT: B 230 TRP cc_start: 0.7582 (t60) cc_final: 0.7335 (t-100) REVERT: B 254 MET cc_start: 0.7946 (ttm) cc_final: 0.7621 (ttm) REVERT: B 397 TRP cc_start: 0.7079 (t-100) cc_final: 0.6766 (t-100) REVERT: B 402 MET cc_start: 0.8167 (mmm) cc_final: 0.7151 (mmm) REVERT: B 462 TRP cc_start: 0.8277 (t-100) cc_final: 0.7991 (t60) REVERT: B 474 ASN cc_start: 0.8606 (m-40) cc_final: 0.8138 (t0) REVERT: B 475 MET cc_start: 0.5185 (mtp) cc_final: 0.4769 (mtp) REVERT: B 519 PHE cc_start: 0.9007 (m-10) cc_final: 0.8440 (m-80) REVERT: B 544 PHE cc_start: 0.8961 (t80) cc_final: 0.8518 (t80) REVERT: B 546 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8840 (mt-10) REVERT: B 551 PHE cc_start: 0.8322 (m-10) cc_final: 0.7070 (m-80) REVERT: C 14 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8081 (tpt170) REVERT: C 58 PHE cc_start: 0.7565 (t80) cc_final: 0.6753 (t80) REVERT: C 138 ARG cc_start: 0.8103 (tmt-80) cc_final: 0.7799 (tpt90) REVERT: C 142 TYR cc_start: 0.8490 (t80) cc_final: 0.7877 (t80) REVERT: C 147 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8879 (mp0) REVERT: C 153 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9020 (mmmt) REVERT: C 164 LEU cc_start: 0.8898 (mt) cc_final: 0.8682 (mt) REVERT: C 250 ASN cc_start: 0.8459 (m-40) cc_final: 0.7792 (m110) REVERT: D 66 MET cc_start: 0.1749 (ttt) cc_final: 0.0864 (tpt) outliers start: 3 outliers final: 2 residues processed: 234 average time/residue: 0.1512 time to fit residues: 46.6343 Evaluate side-chains 173 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 141 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 581 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.074483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058663 restraints weight = 105184.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060088 restraints weight = 71316.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061159 restraints weight = 53343.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061922 restraints weight = 42783.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062507 restraints weight = 36049.310| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13329 Z= 0.204 Angle : 0.894 13.557 18103 Z= 0.455 Chirality : 0.050 0.343 1999 Planarity : 0.008 0.144 2359 Dihedral : 8.704 57.349 1829 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.73 % Favored : 82.02 % Rotamer: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.98 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.18), residues: 1630 helix: -2.27 (0.22), residues: 404 sheet: -2.44 (0.36), residues: 184 loop : -3.54 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 359 TYR 0.027 0.002 TYR C 346 PHE 0.027 0.002 PHE A 55 TRP 0.033 0.002 TRP B 577 HIS 0.011 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00439 (13327) covalent geometry : angle 0.89438 (18103) hydrogen bonds : bond 0.04710 ( 262) hydrogen bonds : angle 6.63691 ( 696) Misc. bond : bond 0.00997 ( 2) *********************** 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 213 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9402 (ttt180) cc_final: 0.8988 (ttp-110) REVERT: A 27 HIS cc_start: 0.9036 (m90) cc_final: 0.8771 (m-70) REVERT: A 50 PHE cc_start: 0.9477 (m-80) cc_final: 0.9139 (m-10) REVERT: A 57 MET cc_start: 0.9094 (mmm) cc_final: 0.8659 (mmm) REVERT: A 104 MET cc_start: 0.8842 (mmt) cc_final: 0.8613 (mmm) REVERT: A 194 MET cc_start: 0.7828 (tpp) cc_final: 0.7460 (tpt) REVERT: A 401 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8568 (mmt180) REVERT: A 402 MET cc_start: 0.9213 (mtm) cc_final: 0.8601 (mtm) REVERT: A 525 ASP cc_start: 0.8144 (m-30) cc_final: 0.7872 (m-30) REVERT: A 542 HIS cc_start: 0.8418 (m90) cc_final: 0.7977 (m170) REVERT: A 547 MET cc_start: 0.8218 (mmm) cc_final: 0.7952 (mmm) REVERT: A 580 ASN cc_start: 0.8960 (p0) cc_final: 0.8476 (p0) REVERT: A 582 ASN cc_start: 0.7370 (m-40) cc_final: 0.6671 (m110) REVERT: B 13 MET cc_start: 0.8952 (ttp) cc_final: 0.8375 (tpt) REVERT: B 61 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8573 (mmt180) REVERT: B 67 ASP cc_start: 0.8171 (p0) cc_final: 0.7963 (p0) REVERT: B 80 TRP cc_start: 0.8128 (t-100) cc_final: 0.7615 (t-100) REVERT: B 254 MET cc_start: 0.8065 (ttm) cc_final: 0.7716 (ttm) REVERT: B 397 TRP cc_start: 0.7136 (t-100) cc_final: 0.6852 (t-100) REVERT: B 402 MET cc_start: 0.8165 (mmm) cc_final: 0.7171 (mmm) REVERT: B 519 PHE cc_start: 0.9168 (m-10) cc_final: 0.8637 (m-80) REVERT: B 544 PHE cc_start: 0.9009 (t80) cc_final: 0.8596 (t80) REVERT: C 14 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7988 (ttt180) REVERT: C 58 PHE cc_start: 0.7593 (t80) cc_final: 0.6816 (t80) REVERT: C 120 ASP cc_start: 0.8772 (m-30) cc_final: 0.8502 (m-30) REVERT: C 142 TYR cc_start: 0.8504 (t80) cc_final: 0.8243 (t80) REVERT: C 153 LYS cc_start: 0.9493 (mmpt) cc_final: 0.9111 (mmmt) REVERT: C 250 ASN cc_start: 0.8543 (m-40) cc_final: 0.7839 (m110) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1573 time to fit residues: 44.3211 Evaluate side-chains 158 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 12 optimal weight: 20.0000 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 0.0010 chunk 78 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 263 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.076937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061017 restraints weight = 102505.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062414 restraints weight = 70632.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063512 restraints weight = 53773.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.064316 restraints weight = 43260.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.064958 restraints weight = 36476.751| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13329 Z= 0.143 Angle : 0.817 14.222 18103 Z= 0.412 Chirality : 0.048 0.316 1999 Planarity : 0.007 0.137 2359 Dihedral : 7.974 54.376 1829 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.72 % Favored : 85.09 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.08 (0.19), residues: 1630 helix: -1.86 (0.23), residues: 395 sheet: -2.16 (0.38), residues: 171 loop : -3.37 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 359 TYR 0.024 0.002 TYR C 346 PHE 0.015 0.002 PHE C 66 TRP 0.023 0.002 TRP B 389 HIS 0.008 0.001 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00317 (13327) covalent geometry : angle 0.81684 (18103) hydrogen bonds : bond 0.04135 ( 262) hydrogen bonds : angle 6.40355 ( 696) Misc. bond : bond 0.00953 ( 2) *********************** 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 214 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.550 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 27 HIS cc_start: 0.8898 (m90) cc_final: 0.8617 (m-70) REVERT: A 50 PHE cc_start: 0.9383 (m-80) cc_final: 0.9148 (m-80) REVERT: A 57 MET cc_start: 0.9092 (mmm) cc_final: 0.8823 (mmm) REVERT: A 102 MET cc_start: 0.6811 (tpp) cc_final: 0.6574 (tpp) REVERT: A 402 MET cc_start: 0.9191 (mtm) cc_final: 0.8576 (mtm) REVERT: A 580 ASN cc_start: 0.9047 (p0) cc_final: 0.8516 (p0) REVERT: A 582 ASN cc_start: 0.7655 (m-40) cc_final: 0.7079 (m-40) REVERT: B 13 MET cc_start: 0.8830 (ttp) cc_final: 0.8154 (tpt) REVERT: B 27 HIS cc_start: 0.8999 (t70) cc_final: 0.8761 (t-90) REVERT: B 80 TRP cc_start: 0.7977 (t-100) cc_final: 0.7222 (t-100) REVERT: B 397 TRP cc_start: 0.7029 (t-100) cc_final: 0.6737 (t-100) REVERT: B 402 MET cc_start: 0.8022 (mmm) cc_final: 0.7104 (mmm) REVERT: B 474 ASN cc_start: 0.8693 (p0) cc_final: 0.8241 (p0) REVERT: B 475 MET cc_start: 0.4972 (mtp) cc_final: 0.4695 (mtp) REVERT: B 519 PHE cc_start: 0.9154 (m-10) cc_final: 0.8676 (m-80) REVERT: C 14 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7946 (ttt180) REVERT: C 138 ARG cc_start: 0.8122 (tmt-80) cc_final: 0.7883 (tpt90) REVERT: C 153 LYS cc_start: 0.9521 (mmpt) cc_final: 0.9143 (mmmt) REVERT: C 184 LEU cc_start: 0.9753 (tt) cc_final: 0.9467 (tp) REVERT: C 222 LEU cc_start: 0.8941 (mt) cc_final: 0.8678 (mp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1661 time to fit residues: 46.8147 Evaluate side-chains 168 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 37 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 98 optimal weight: 40.0000 chunk 161 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 overall best weight: 3.1184 ------------------------------------------------------------------------------- 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 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 37 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN D 134 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.075630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058531 restraints weight = 102025.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.059956 restraints weight = 70158.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061000 restraints weight = 53344.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061821 restraints weight = 43302.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062441 restraints weight = 36928.630| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13329 Z= 0.159 Angle : 0.805 13.870 18103 Z= 0.408 Chirality : 0.048 0.272 1999 Planarity : 0.007 0.145 2359 Dihedral : 7.746 55.797 1829 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.81 % Favored : 83.01 % Rotamer: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.86 (0.19), residues: 1630 helix: -1.63 (0.24), residues: 388 sheet: -2.10 (0.39), residues: 165 loop : -3.22 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 359 TYR 0.018 0.002 TYR B 555 PHE 0.051 0.002 PHE B 551 TRP 0.025 0.002 TRP A 577 HIS 0.011 0.001 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00351 (13327) covalent geometry : angle 0.80541 (18103) hydrogen bonds : bond 0.03788 ( 262) hydrogen bonds : angle 6.17474 ( 696) Misc. bond : bond 0.00850 ( 2) *********************** 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 200 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.513 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: A 27 HIS cc_start: 0.8811 (m90) cc_final: 0.8559 (m-70) REVERT: A 57 MET cc_start: 0.9164 (mmm) cc_final: 0.8786 (mmm) REVERT: A 78 MET cc_start: 0.8558 (mmp) cc_final: 0.8004 (mmm) REVERT: A 193 MET cc_start: 0.9009 (tpt) cc_final: 0.8764 (tpp) REVERT: A 194 MET cc_start: 0.7247 (tpt) cc_final: 0.6903 (tpt) REVERT: A 321 TYR cc_start: 0.8554 (p90) cc_final: 0.8287 (p90) REVERT: A 402 MET cc_start: 0.9217 (mtm) cc_final: 0.8360 (mtm) REVERT: A 533 ASN cc_start: 0.8205 (t0) cc_final: 0.7324 (m-40) REVERT: A 542 HIS cc_start: 0.8378 (m90) cc_final: 0.7849 (m170) REVERT: A 580 ASN cc_start: 0.8976 (p0) cc_final: 0.8380 (p0) REVERT: A 582 ASN cc_start: 0.7558 (m-40) cc_final: 0.6949 (m-40) REVERT: B 13 MET cc_start: 0.8812 (ttp) cc_final: 0.8078 (tpt) REVERT: B 27 HIS cc_start: 0.8982 (t70) cc_final: 0.8765 (t-90) REVERT: B 66 ASP cc_start: 0.8972 (t70) cc_final: 0.8757 (t0) REVERT: B 67 ASP cc_start: 0.8337 (p0) cc_final: 0.8035 (p0) REVERT: B 80 TRP cc_start: 0.7998 (t-100) cc_final: 0.7564 (t-100) REVERT: B 102 MET cc_start: 0.8616 (mmp) cc_final: 0.8222 (ppp) REVERT: B 397 TRP cc_start: 0.7033 (t-100) cc_final: 0.6800 (t-100) REVERT: B 402 MET cc_start: 0.8134 (mmm) cc_final: 0.7112 (mmm) REVERT: B 474 ASN cc_start: 0.8680 (p0) cc_final: 0.8289 (p0) REVERT: B 475 MET cc_start: 0.4909 (mtp) cc_final: 0.4462 (mtp) REVERT: B 543 LEU cc_start: 0.9167 (tp) cc_final: 0.8860 (tp) REVERT: B 578 LYS cc_start: 0.9175 (mttt) cc_final: 0.8606 (mptt) REVERT: C 138 ARG cc_start: 0.8186 (tmt-80) cc_final: 0.7809 (tpt90) REVERT: C 142 TYR cc_start: 0.8386 (t80) cc_final: 0.7958 (t80) REVERT: C 153 LYS cc_start: 0.9534 (mmpt) cc_final: 0.9190 (mmmt) REVERT: C 184 LEU cc_start: 0.9697 (tt) cc_final: 0.9419 (tp) REVERT: C 192 ARG cc_start: 0.4168 (mtt-85) cc_final: 0.1871 (mtt-85) REVERT: C 222 LEU cc_start: 0.8798 (mt) cc_final: 0.8433 (mp) REVERT: D 97 GLU cc_start: 0.8659 (pp20) cc_final: 0.8079 (tm-30) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.1520 time to fit residues: 40.4953 Evaluate side-chains 166 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 84 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 chunk 55 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 overall best weight: 1.6020 ------------------------------------------------------------------------------- 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 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 53 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.076417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060167 restraints weight = 103199.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.061631 restraints weight = 70553.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.062731 restraints weight = 53003.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.063553 restraints weight = 42595.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064110 restraints weight = 36065.747| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13329 Z= 0.131 Angle : 0.778 14.765 18103 Z= 0.390 Chirality : 0.047 0.329 1999 Planarity : 0.007 0.138 2359 Dihedral : 7.428 56.434 1829 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.60 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.20), residues: 1630 helix: -1.34 (0.25), residues: 385 sheet: -2.00 (0.38), residues: 174 loop : -3.20 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.017 0.001 TYR B 240 PHE 0.042 0.002 PHE B 551 TRP 0.017 0.002 TRP C 49 HIS 0.008 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00292 (13327) covalent geometry : angle 0.77784 (18103) hydrogen bonds : bond 0.03626 ( 262) hydrogen bonds : angle 6.06602 ( 696) Misc. bond : bond 0.00723 ( 2) *********************** 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 201 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.596 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: A 27 HIS cc_start: 0.8768 (m90) cc_final: 0.8515 (m-70) REVERT: A 57 MET cc_start: 0.9073 (mmm) cc_final: 0.8698 (mmm) REVERT: A 78 MET cc_start: 0.8502 (mmp) cc_final: 0.8021 (mmm) REVERT: A 321 TYR cc_start: 0.8538 (p90) cc_final: 0.8338 (p90) REVERT: A 402 MET cc_start: 0.9143 (mtm) cc_final: 0.8552 (mtm) REVERT: A 542 HIS cc_start: 0.8340 (m90) cc_final: 0.7895 (m170) REVERT: A 580 ASN cc_start: 0.8950 (p0) cc_final: 0.8415 (p0) REVERT: A 582 ASN cc_start: 0.7551 (m-40) cc_final: 0.6988 (m-40) REVERT: B 13 MET cc_start: 0.8634 (ttp) cc_final: 0.7893 (tpp) REVERT: B 27 HIS cc_start: 0.8997 (t70) cc_final: 0.8781 (t-90) REVERT: B 66 ASP cc_start: 0.8979 (t70) cc_final: 0.8754 (t0) REVERT: B 67 ASP cc_start: 0.8288 (p0) cc_final: 0.8069 (p0) REVERT: B 80 TRP cc_start: 0.7846 (t-100) cc_final: 0.7036 (t-100) REVERT: B 102 MET cc_start: 0.8774 (mmp) cc_final: 0.8523 (ppp) REVERT: B 397 TRP cc_start: 0.6911 (t-100) cc_final: 0.6663 (t-100) REVERT: B 402 MET cc_start: 0.7960 (mmm) cc_final: 0.7112 (mmm) REVERT: B 474 ASN cc_start: 0.8657 (p0) cc_final: 0.8248 (p0) REVERT: B 475 MET cc_start: 0.4824 (mtp) cc_final: 0.4448 (mtp) REVERT: B 519 PHE cc_start: 0.8708 (m-80) cc_final: 0.7892 (m-80) REVERT: B 543 LEU cc_start: 0.9184 (tp) cc_final: 0.8895 (tp) REVERT: C 36 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9166 (mm-30) REVERT: C 138 ARG cc_start: 0.8029 (tmt-80) cc_final: 0.7693 (tpt90) REVERT: C 142 TYR cc_start: 0.8274 (t80) cc_final: 0.7801 (t80) REVERT: C 153 LYS cc_start: 0.9562 (mmpt) cc_final: 0.9243 (mmmt) REVERT: C 172 ASN cc_start: 0.9152 (m-40) cc_final: 0.8901 (m110) REVERT: C 184 LEU cc_start: 0.9703 (tt) cc_final: 0.9410 (tp) REVERT: C 192 ARG cc_start: 0.3954 (mtt-85) cc_final: 0.1711 (mtt-85) REVERT: C 222 LEU cc_start: 0.8865 (mt) cc_final: 0.8609 (mp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1504 time to fit residues: 40.0337 Evaluate side-chains 163 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 23 optimal weight: 0.0050 chunk 94 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 139 optimal weight: 0.0970 chunk 75 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.5196 ------------------------------------------------------------------------------- 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 569 GLN ** A 581 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 510 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.076072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060019 restraints weight = 105323.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.061489 restraints weight = 72098.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062540 restraints weight = 54416.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063348 restraints weight = 43841.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063909 restraints weight = 37101.570| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13329 Z= 0.141 Angle : 0.786 14.541 18103 Z= 0.393 Chirality : 0.048 0.326 1999 Planarity : 0.007 0.136 2359 Dihedral : 7.308 57.822 1829 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.77 % Favored : 84.11 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.19), residues: 1630 helix: -1.47 (0.24), residues: 400 sheet: -1.80 (0.40), residues: 163 loop : -3.25 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 359 TYR 0.019 0.001 TYR C 346 PHE 0.043 0.002 PHE B 551 TRP 0.016 0.002 TRP C 49 HIS 0.011 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00315 (13327) covalent geometry : angle 0.78606 (18103) hydrogen bonds : bond 0.03598 ( 262) hydrogen bonds : angle 5.99058 ( 696) Misc. bond : bond 0.00680 ( 2) *********************** 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 196 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.341 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 27 HIS cc_start: 0.8816 (m90) cc_final: 0.8573 (m-70) REVERT: A 57 MET cc_start: 0.9063 (mmm) cc_final: 0.8484 (mmm) REVERT: A 78 MET cc_start: 0.8495 (mmp) cc_final: 0.8149 (mmm) REVERT: A 102 MET cc_start: 0.6014 (tpp) cc_final: 0.5802 (tpp) REVERT: A 253 PHE cc_start: 0.7361 (m-10) cc_final: 0.7137 (m-80) REVERT: A 321 TYR cc_start: 0.8482 (p90) cc_final: 0.8244 (p90) REVERT: A 402 MET cc_start: 0.9164 (mtm) cc_final: 0.8548 (mtm) REVERT: A 515 PHE cc_start: 0.8230 (t80) cc_final: 0.7543 (t80) REVERT: A 517 LYS cc_start: 0.9336 (mttt) cc_final: 0.8861 (mttp) REVERT: A 542 HIS cc_start: 0.8452 (m90) cc_final: 0.7948 (m170) REVERT: A 580 ASN cc_start: 0.8995 (p0) cc_final: 0.8462 (p0) REVERT: A 582 ASN cc_start: 0.7741 (m-40) cc_final: 0.7106 (m-40) REVERT: B 13 MET cc_start: 0.8648 (ttp) cc_final: 0.7702 (tpp) REVERT: B 27 HIS cc_start: 0.8986 (t70) cc_final: 0.8786 (t70) REVERT: B 66 ASP cc_start: 0.8982 (t70) cc_final: 0.8751 (t0) REVERT: B 67 ASP cc_start: 0.8372 (p0) cc_final: 0.8107 (p0) REVERT: B 80 TRP cc_start: 0.7924 (t-100) cc_final: 0.7451 (t-100) REVERT: B 102 MET cc_start: 0.8831 (mmp) cc_final: 0.8260 (ppp) REVERT: B 237 PHE cc_start: 0.8889 (t80) cc_final: 0.8635 (t80) REVERT: B 397 TRP cc_start: 0.6977 (t-100) cc_final: 0.6704 (t-100) REVERT: B 402 MET cc_start: 0.7936 (mmm) cc_final: 0.7125 (mmm) REVERT: B 474 ASN cc_start: 0.8691 (p0) cc_final: 0.8275 (p0) REVERT: B 475 MET cc_start: 0.4894 (mtp) cc_final: 0.4425 (mtp) REVERT: B 519 PHE cc_start: 0.8753 (m-80) cc_final: 0.7775 (m-80) REVERT: B 521 LEU cc_start: 0.7894 (mt) cc_final: 0.7689 (mp) REVERT: B 543 LEU cc_start: 0.9193 (tp) cc_final: 0.8902 (tp) REVERT: B 547 MET cc_start: 0.8273 (mmt) cc_final: 0.8036 (mmm) REVERT: B 565 THR cc_start: 0.6131 (p) cc_final: 0.5786 (p) REVERT: C 36 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9146 (mm-30) REVERT: C 91 MET cc_start: 0.4603 (ptp) cc_final: 0.3159 (mmm) REVERT: C 138 ARG cc_start: 0.8116 (tmt-80) cc_final: 0.7753 (tpt90) REVERT: C 142 TYR cc_start: 0.8292 (t80) cc_final: 0.7822 (t80) REVERT: C 153 LYS cc_start: 0.9581 (mmpt) cc_final: 0.9261 (mmmt) REVERT: C 172 ASN cc_start: 0.9172 (m-40) cc_final: 0.8954 (m110) REVERT: C 184 LEU cc_start: 0.9707 (tt) cc_final: 0.9363 (tp) REVERT: C 192 ARG cc_start: 0.4016 (mtt-85) cc_final: 0.1849 (mtt-85) REVERT: C 195 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 222 LEU cc_start: 0.9003 (mt) cc_final: 0.8737 (mp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1532 time to fit residues: 39.8234 Evaluate side-chains 163 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 89 optimal weight: 0.0570 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN 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 103 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.075889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058033 restraints weight = 100942.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059399 restraints weight = 70131.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.060352 restraints weight = 53921.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061215 restraints weight = 44466.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061707 restraints weight = 38173.226| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13329 Z= 0.144 Angle : 0.785 14.677 18103 Z= 0.392 Chirality : 0.048 0.279 1999 Planarity : 0.007 0.132 2359 Dihedral : 7.213 59.254 1829 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.89 % Favored : 83.99 % Rotamer: Outliers : 0.07 % Allowed : 1.29 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.19), residues: 1630 helix: -1.54 (0.24), residues: 400 sheet: -1.86 (0.38), residues: 173 loop : -3.19 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 163 TYR 0.019 0.001 TYR C 346 PHE 0.039 0.002 PHE B 551 TRP 0.032 0.002 TRP C 49 HIS 0.009 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00323 (13327) covalent geometry : angle 0.78476 (18103) hydrogen bonds : bond 0.03605 ( 262) hydrogen bonds : angle 5.91847 ( 696) Misc. bond : bond 0.00628 ( 2) *********************** 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 191 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.506 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: A 27 HIS cc_start: 0.8776 (m90) cc_final: 0.8534 (m-70) REVERT: A 57 MET cc_start: 0.9057 (mmm) cc_final: 0.8468 (mmm) REVERT: A 78 MET cc_start: 0.8179 (mmp) cc_final: 0.7908 (mmm) REVERT: A 193 MET cc_start: 0.8948 (tpt) cc_final: 0.8746 (tpp) REVERT: A 194 MET cc_start: 0.7368 (tpt) cc_final: 0.7129 (tpt) REVERT: A 321 TYR cc_start: 0.8503 (p90) cc_final: 0.8182 (p90) REVERT: A 402 MET cc_start: 0.9178 (mtm) cc_final: 0.8540 (mtm) REVERT: A 515 PHE cc_start: 0.8069 (t80) cc_final: 0.7446 (t80) REVERT: A 517 LYS cc_start: 0.9306 (mttt) cc_final: 0.8798 (mttp) REVERT: A 542 HIS cc_start: 0.8353 (m90) cc_final: 0.7899 (m170) REVERT: A 580 ASN cc_start: 0.8961 (p0) cc_final: 0.8517 (p0) REVERT: A 582 ASN cc_start: 0.7802 (m-40) cc_final: 0.7112 (m-40) REVERT: B 13 MET cc_start: 0.8609 (ttp) cc_final: 0.7845 (tpp) REVERT: B 66 ASP cc_start: 0.9045 (t70) cc_final: 0.8755 (m-30) REVERT: B 67 ASP cc_start: 0.8351 (p0) cc_final: 0.8030 (p0) REVERT: B 80 TRP cc_start: 0.7903 (t-100) cc_final: 0.7464 (t-100) REVERT: B 102 MET cc_start: 0.8465 (mmp) cc_final: 0.8162 (ppp) REVERT: B 170 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8811 (pp30) REVERT: B 402 MET cc_start: 0.7964 (mmm) cc_final: 0.7050 (mmm) REVERT: B 474 ASN cc_start: 0.8683 (p0) cc_final: 0.8288 (p0) REVERT: B 475 MET cc_start: 0.4860 (mtp) cc_final: 0.4350 (mtp) REVERT: B 519 PHE cc_start: 0.8744 (m-80) cc_final: 0.7813 (m-80) REVERT: B 521 LEU cc_start: 0.7987 (mt) cc_final: 0.7707 (mp) REVERT: B 543 LEU cc_start: 0.9137 (tp) cc_final: 0.8895 (tp) REVERT: B 547 MET cc_start: 0.8296 (mmt) cc_final: 0.8067 (mmm) REVERT: C 36 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9172 (mm-30) REVERT: C 91 MET cc_start: 0.4248 (ptp) cc_final: 0.2812 (mmt) REVERT: C 135 ARG cc_start: 0.8454 (mmt180) cc_final: 0.8223 (mmt180) REVERT: C 138 ARG cc_start: 0.8123 (tmt-80) cc_final: 0.7833 (tpt90) REVERT: C 142 TYR cc_start: 0.8250 (t80) cc_final: 0.7774 (t80) REVERT: C 153 LYS cc_start: 0.9529 (mmpt) cc_final: 0.9236 (mmmt) REVERT: C 172 ASN cc_start: 0.9254 (m-40) cc_final: 0.9035 (m110) REVERT: C 184 LEU cc_start: 0.9687 (tt) cc_final: 0.9368 (tp) REVERT: C 192 ARG cc_start: 0.4073 (mtt-85) cc_final: 0.1897 (mtt-85) REVERT: C 222 LEU cc_start: 0.8867 (mt) cc_final: 0.8591 (mp) REVERT: D 66 MET cc_start: 0.2321 (ttt) cc_final: 0.1970 (tpt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1572 time to fit residues: 39.7456 Evaluate side-chains 162 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 21 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.074903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056954 restraints weight = 101835.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058246 restraints weight = 72044.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.059264 restraints weight = 56053.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059926 restraints weight = 46387.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060558 restraints weight = 40168.652| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13329 Z= 0.166 Angle : 0.811 14.001 18103 Z= 0.404 Chirality : 0.047 0.269 1999 Planarity : 0.007 0.128 2359 Dihedral : 7.228 59.519 1829 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.99 % Favored : 82.88 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.73 (0.20), residues: 1630 helix: -1.59 (0.24), residues: 401 sheet: -1.72 (0.39), residues: 172 loop : -3.18 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 355 TYR 0.020 0.002 TYR C 346 PHE 0.036 0.002 PHE B 55 TRP 0.047 0.003 TRP B 397 HIS 0.010 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00368 (13327) covalent geometry : angle 0.81141 (18103) hydrogen bonds : bond 0.03663 ( 262) hydrogen bonds : angle 6.04357 ( 696) Misc. bond : bond 0.00666 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.521 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 27 HIS cc_start: 0.8744 (m90) cc_final: 0.8473 (m-70) REVERT: A 57 MET cc_start: 0.9000 (mmm) cc_final: 0.8386 (mmm) REVERT: A 193 MET cc_start: 0.8894 (tpt) cc_final: 0.8657 (tpp) REVERT: A 194 MET cc_start: 0.7380 (tpt) cc_final: 0.7064 (tpt) REVERT: A 402 MET cc_start: 0.9135 (mtm) cc_final: 0.8557 (mtm) REVERT: A 515 PHE cc_start: 0.7987 (t80) cc_final: 0.7388 (t80) REVERT: A 517 LYS cc_start: 0.9293 (mttt) cc_final: 0.8774 (mttp) REVERT: A 542 HIS cc_start: 0.8334 (m90) cc_final: 0.7906 (m170) REVERT: A 580 ASN cc_start: 0.8984 (p0) cc_final: 0.8555 (p0) REVERT: A 582 ASN cc_start: 0.7855 (m-40) cc_final: 0.7151 (m-40) REVERT: B 13 MET cc_start: 0.8487 (ttp) cc_final: 0.7377 (tpp) REVERT: B 66 ASP cc_start: 0.9047 (t70) cc_final: 0.8743 (m-30) REVERT: B 67 ASP cc_start: 0.8450 (p0) cc_final: 0.8153 (p0) REVERT: B 80 TRP cc_start: 0.7895 (t-100) cc_final: 0.7454 (t-100) REVERT: B 102 MET cc_start: 0.8243 (mmp) cc_final: 0.7876 (ppp) REVERT: B 254 MET cc_start: 0.7224 (ttm) cc_final: 0.7022 (ttp) REVERT: B 397 TRP cc_start: 0.6641 (t-100) cc_final: 0.6261 (t-100) REVERT: B 402 MET cc_start: 0.8211 (mmm) cc_final: 0.7669 (mpp) REVERT: B 467 HIS cc_start: 0.7989 (t-170) cc_final: 0.7766 (t-90) REVERT: B 474 ASN cc_start: 0.8608 (p0) cc_final: 0.8238 (p0) REVERT: B 475 MET cc_start: 0.4833 (mtp) cc_final: 0.4361 (mtp) REVERT: B 519 PHE cc_start: 0.8747 (m-80) cc_final: 0.7825 (m-80) REVERT: B 521 LEU cc_start: 0.8029 (mt) cc_final: 0.7720 (mp) REVERT: C 36 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9109 (mm-30) REVERT: C 64 MET cc_start: 0.2165 (mtt) cc_final: 0.1712 (mtm) REVERT: C 91 MET cc_start: 0.3772 (ptp) cc_final: 0.2215 (mmt) REVERT: C 101 PRO cc_start: 0.9243 (Cg_exo) cc_final: 0.8838 (Cg_endo) REVERT: C 142 TYR cc_start: 0.8226 (t80) cc_final: 0.7777 (t80) REVERT: C 153 LYS cc_start: 0.9512 (mmpt) cc_final: 0.9202 (mmmt) REVERT: C 164 LEU cc_start: 0.8241 (mt) cc_final: 0.7707 (mt) REVERT: C 172 ASN cc_start: 0.9230 (m-40) cc_final: 0.9021 (m110) REVERT: C 184 LEU cc_start: 0.9699 (tt) cc_final: 0.9389 (tp) REVERT: C 192 ARG cc_start: 0.4184 (mtt-85) cc_final: 0.2007 (mtt-85) REVERT: C 222 LEU cc_start: 0.8878 (mt) cc_final: 0.8601 (mp) REVERT: D 66 MET cc_start: 0.2103 (ttt) cc_final: 0.1760 (tpt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1526 time to fit residues: 37.8289 Evaluate side-chains 152 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 25 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 3.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.074903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057206 restraints weight = 102505.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058562 restraints weight = 70977.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059574 restraints weight = 54299.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.060359 restraints weight = 44676.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060841 restraints weight = 38455.854| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13329 Z= 0.169 Angle : 0.823 13.792 18103 Z= 0.408 Chirality : 0.049 0.359 1999 Planarity : 0.008 0.126 2359 Dihedral : 7.283 59.995 1829 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.50 % Favored : 83.44 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 1.90 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.19), residues: 1630 helix: -1.74 (0.23), residues: 414 sheet: -1.62 (0.41), residues: 162 loop : -3.19 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 355 TYR 0.020 0.001 TYR C 346 PHE 0.030 0.002 PHE B 551 TRP 0.031 0.003 TRP A 168 HIS 0.009 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00377 (13327) covalent geometry : angle 0.82293 (18103) hydrogen bonds : bond 0.03691 ( 262) hydrogen bonds : angle 6.05536 ( 696) Misc. bond : bond 0.00632 ( 2) ********************** 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 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.517 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: A 27 HIS cc_start: 0.8771 (m90) cc_final: 0.8473 (m-70) REVERT: A 50 PHE cc_start: 0.9502 (m-80) cc_final: 0.9172 (m-80) REVERT: A 57 MET cc_start: 0.9023 (mmm) cc_final: 0.8392 (mmm) REVERT: A 193 MET cc_start: 0.8931 (tpt) cc_final: 0.8683 (tpp) REVERT: A 194 MET cc_start: 0.7371 (tpt) cc_final: 0.7102 (tpt) REVERT: A 402 MET cc_start: 0.9125 (mtm) cc_final: 0.8558 (mtm) REVERT: A 515 PHE cc_start: 0.7932 (t80) cc_final: 0.7315 (t80) REVERT: A 517 LYS cc_start: 0.9295 (mttt) cc_final: 0.8786 (mttp) REVERT: A 580 ASN cc_start: 0.9005 (p0) cc_final: 0.8556 (p0) REVERT: A 582 ASN cc_start: 0.7908 (m-40) cc_final: 0.7134 (m-40) REVERT: B 13 MET cc_start: 0.8458 (ttp) cc_final: 0.7478 (tpp) REVERT: B 66 ASP cc_start: 0.8998 (t70) cc_final: 0.8695 (m-30) REVERT: B 67 ASP cc_start: 0.8467 (p0) cc_final: 0.8186 (p0) REVERT: B 80 TRP cc_start: 0.7920 (t-100) cc_final: 0.7212 (t-100) REVERT: B 102 MET cc_start: 0.8332 (mmp) cc_final: 0.7864 (ppp) REVERT: B 397 TRP cc_start: 0.6571 (t-100) cc_final: 0.6070 (t-100) REVERT: B 402 MET cc_start: 0.8154 (mmm) cc_final: 0.7556 (mpp) REVERT: B 474 ASN cc_start: 0.8623 (p0) cc_final: 0.8354 (p0) REVERT: B 475 MET cc_start: 0.4763 (mtp) cc_final: 0.4264 (mtm) REVERT: B 519 PHE cc_start: 0.8791 (m-80) cc_final: 0.7870 (m-80) REVERT: B 521 LEU cc_start: 0.8054 (mt) cc_final: 0.7675 (mp) REVERT: B 543 LEU cc_start: 0.9192 (tp) cc_final: 0.8876 (tp) REVERT: C 36 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9067 (mm-30) REVERT: C 64 MET cc_start: 0.2071 (mtt) cc_final: 0.1654 (mtm) REVERT: C 91 MET cc_start: 0.3951 (ptp) cc_final: 0.2568 (mmt) REVERT: C 101 PRO cc_start: 0.9121 (Cg_exo) cc_final: 0.8749 (Cg_endo) REVERT: C 142 TYR cc_start: 0.8221 (t80) cc_final: 0.7780 (t80) REVERT: C 153 LYS cc_start: 0.9496 (mmpt) cc_final: 0.9172 (mmmt) REVERT: C 163 ARG cc_start: 0.8651 (tmm160) cc_final: 0.8371 (tmt170) REVERT: C 164 LEU cc_start: 0.8245 (mt) cc_final: 0.7485 (mt) REVERT: C 172 ASN cc_start: 0.9292 (m-40) cc_final: 0.9076 (m110) REVERT: C 184 LEU cc_start: 0.9724 (tt) cc_final: 0.9378 (tp) REVERT: C 192 ARG cc_start: 0.4133 (mtt-85) cc_final: 0.1955 (mtt-85) REVERT: C 222 LEU cc_start: 0.8854 (mt) cc_final: 0.8653 (mp) REVERT: D 66 MET cc_start: 0.2143 (ttt) cc_final: 0.1819 (tpt) REVERT: D 69 THR cc_start: 0.3068 (t) cc_final: 0.2844 (t) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1664 time to fit residues: 40.9031 Evaluate side-chains 156 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 0.0050 chunk 68 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 overall best weight: 4.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN B 27 HIS ** 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055316 restraints weight = 100308.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056613 restraints weight = 71249.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.057614 restraints weight = 55523.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058068 restraints weight = 46356.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.058779 restraints weight = 41472.382| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13329 Z= 0.190 Angle : 0.853 13.435 18103 Z= 0.424 Chirality : 0.048 0.274 1999 Planarity : 0.008 0.125 2359 Dihedral : 7.358 60.551 1829 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.55 % Favored : 82.33 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.95 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.89 (0.19), residues: 1630 helix: -1.95 (0.23), residues: 417 sheet: -1.73 (0.40), residues: 175 loop : -3.21 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 550 TYR 0.022 0.002 TYR C 346 PHE 0.050 0.003 PHE B 55 TRP 0.032 0.003 TRP A 168 HIS 0.022 0.002 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00415 (13327) covalent geometry : angle 0.85255 (18103) hydrogen bonds : bond 0.03705 ( 262) hydrogen bonds : angle 6.16915 ( 696) Misc. bond : bond 0.00640 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.44 seconds wall clock time: 41 minutes 43.92 seconds (2503.92 seconds total)