Starting phenix.real_space_refine on Mon Mar 11 17:31:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/03_2024/8p4x_17429_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.189 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 5564 2.51 5 N 1456 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 497": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "B" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 5.06, per 1000 atoms: 0.58 Number of scatterers: 8756 At special positions: 0 Unit cell: (95.682, 104.302, 95.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 4 15.00 Mg 2 11.99 O 1652 8.00 N 1456 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 2 sheets defined 47.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.626A pdb=" N LYS A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 120 removed outlier: 4.228A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.589A pdb=" N GLN A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Proline residue: A 137 - end of helix removed outlier: 3.822A pdb=" N LYS A 140 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 141 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 143 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 144 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.871A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 221 through 224 No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 245 through 264 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 294 through 308 removed outlier: 3.559A pdb=" N HIS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.543A pdb=" N THR A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 320 through 331 removed outlier: 4.026A pdb=" N ARG A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.555A pdb=" N CYS A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.648A pdb=" N GLU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.093A pdb=" N ALA A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.614A pdb=" N TYR A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.588A pdb=" N SER A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 78 through 98 removed outlier: 3.627A pdb=" N LYS B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 120 removed outlier: 4.228A pdb=" N LYS B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.588A pdb=" N GLN B 136 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Proline residue: B 137 - end of helix removed outlier: 3.822A pdb=" N LYS B 140 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 141 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 143 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 144 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.871A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 231 through 234 No H-bonds generated for 'chain 'B' and resid 231 through 234' Processing helix chain 'B' and resid 245 through 264 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.559A pdb=" N HIS B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.543A pdb=" N THR B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 320 through 331 removed outlier: 4.025A pdb=" N ARG B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 330 " --> pdb=" O TYR B 326 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.556A pdb=" N CYS B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.648A pdb=" N GLU B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 4.093A pdb=" N ALA B 425 " --> pdb=" O TRP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.615A pdb=" N TYR B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 506 through 523 removed outlier: 3.587A pdb=" N SER B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 Processing sheet with id= A, first strand: chain 'A' and resid 152 through 156 removed outlier: 3.580A pdb=" N ARG A 124 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU A 128 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 59 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS A 36 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 61 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE A 38 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 63 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR A 103 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TRP A 66 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 105 " --> pdb=" O TRP A 66 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 152 through 156 removed outlier: 3.580A pdb=" N ARG B 124 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 128 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU B 59 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS B 36 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR B 61 " --> pdb=" O HIS B 36 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE B 38 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 63 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR B 103 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TRP B 66 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 105 " --> pdb=" O TRP B 66 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2744 1.34 - 1.46: 2088 1.46 - 1.58: 4014 1.58 - 1.69: 4 1.69 - 1.81: 114 Bond restraints: 8964 Sorted by residual: bond pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5' FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5B FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.49e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.08: 325 106.08 - 113.07: 4584 113.07 - 120.06: 3345 120.06 - 127.05: 3726 127.05 - 134.05: 214 Bond angle restraints: 12194 Sorted by residual: angle pdb=" O1P FAD B 601 " pdb=" P FAD B 601 " pdb=" O2P FAD B 601 " ideal model delta sigma weight residual 122.50 115.09 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" O1P FAD A 601 " pdb=" P FAD A 601 " pdb=" O2P FAD A 601 " ideal model delta sigma weight residual 122.50 115.10 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O5B FAD B 601 " ideal model delta sigma weight residual 104.10 111.17 -7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O5B FAD A 601 " ideal model delta sigma weight residual 104.10 111.16 -7.06 3.00e+00 1.11e-01 5.54e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O2A FAD B 601 " ideal model delta sigma weight residual 121.20 114.74 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 12189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 5002 18.12 - 36.25: 212 36.25 - 54.37: 62 54.37 - 72.50: 30 72.50 - 90.62: 12 Dihedral angle restraints: 5318 sinusoidal: 2270 harmonic: 3048 Sorted by residual: dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 39 " pdb=" C ARG A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 -152.39 90.62 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 662 0.025 - 0.049: 346 0.049 - 0.074: 114 0.074 - 0.098: 42 0.098 - 0.123: 56 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL B 33 " pdb=" N VAL B 33 " pdb=" C VAL B 33 " pdb=" CB VAL B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" C2B FAD A 601 " pdb=" C1B FAD A 601 " pdb=" C3B FAD A 601 " pdb=" O2B FAD A 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1217 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 526 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 526 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 533 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 534 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.017 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.23: 7741 3.23 - 3.78: 12586 3.78 - 4.34: 18822 4.34 - 4.90: 30867 Nonbonded interactions: 70136 Sorted by model distance: nonbonded pdb=" O HOH B 717 " pdb=" O HOH B 740 " model vdw 2.112 2.440 nonbonded pdb=" O HOH A 717 " pdb=" O HOH A 740 " model vdw 2.114 2.440 nonbonded pdb=" OD2 ASP B 420 " pdb=" O HOH B 701 " model vdw 2.116 2.440 nonbonded pdb=" OD2 ASP A 420 " pdb=" O HOH A 701 " model vdw 2.116 2.440 nonbonded pdb=" NH1 ARG A 324 " pdb=" O HOH A 701 " model vdw 2.125 2.520 ... (remaining 70131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 individual isotropic 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.420 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.880 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.004 0.075 8964 Z= 0.273 Angle : 0.561 7.407 12194 Z= 0.284 Chirality : 0.040 0.123 1220 Planarity : 0.004 0.040 1552 Dihedral : 13.116 90.621 3362 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1048 helix: 0.99 (0.24), residues: 528 sheet: 0.00 (0.58), residues: 70 loop : -1.38 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE B 543 TYR 0.012 0.001 TYR B 326 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.105 Fit side-chains REVERT: A 115 GLN cc_start: 0.7079 (tt0) cc_final: 0.6857 (tt0) REVERT: A 200 ASP cc_start: 0.7123 (t70) cc_final: 0.6896 (t0) REVERT: B 115 GLN cc_start: 0.7076 (tt0) cc_final: 0.6854 (tt0) REVERT: B 200 ASP cc_start: 0.7121 (t70) cc_final: 0.6893 (t0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.3060 time to fit residues: 201.2144 Evaluate side-chains 127 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8964 Z= 0.174 Angle : 0.555 7.165 12194 Z= 0.275 Chirality : 0.043 0.160 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.499 90.710 1232 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.43 % Allowed : 9.07 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1048 helix: 1.16 (0.24), residues: 528 sheet: 0.08 (0.57), residues: 70 loop : -1.12 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.012 0.002 PHE A 201 TYR 0.008 0.001 TYR A 451 ARG 0.003 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.082 Fit side-chains REVERT: A 275 ASP cc_start: 0.7912 (t0) cc_final: 0.7666 (t0) REVERT: B 275 ASP cc_start: 0.7913 (t0) cc_final: 0.7672 (t0) outliers start: 4 outliers final: 3 residues processed: 141 average time/residue: 1.4541 time to fit residues: 216.6728 Evaluate side-chains 135 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 36 HIS A 136 GLN A 538 ASN B 32 HIS B 36 HIS B 136 GLN B 538 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8964 Z= 0.350 Angle : 0.721 9.354 12194 Z= 0.368 Chirality : 0.050 0.156 1220 Planarity : 0.006 0.041 1552 Dihedral : 11.314 113.960 1232 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.59 % Allowed : 8.21 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1048 helix: 0.57 (0.22), residues: 520 sheet: 0.07 (0.58), residues: 70 loop : -1.28 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 430 HIS 0.006 0.002 HIS A 385 PHE 0.017 0.003 PHE A 543 TYR 0.013 0.002 TYR A 465 ARG 0.003 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.989 Fit side-chains REVERT: A 114 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7539 (ttpt) REVERT: A 118 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: A 188 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 229 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6567 (pt0) REVERT: A 341 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5326 (mp0) REVERT: B 114 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7545 (ttpt) REVERT: B 118 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: B 188 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 229 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6578 (pt0) REVERT: B 341 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5317 (mp0) outliers start: 24 outliers final: 10 residues processed: 143 average time/residue: 1.4919 time to fit residues: 224.9692 Evaluate side-chains 144 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 538 ASN B 32 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8964 Z= 0.147 Angle : 0.513 7.217 12194 Z= 0.253 Chirality : 0.041 0.119 1220 Planarity : 0.005 0.036 1552 Dihedral : 9.436 106.733 1232 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.30 % Allowed : 10.48 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1048 helix: 0.87 (0.23), residues: 528 sheet: 0.32 (0.58), residues: 70 loop : -1.09 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 430 HIS 0.003 0.001 HIS B 45 PHE 0.010 0.001 PHE B 543 TYR 0.008 0.001 TYR B 326 ARG 0.002 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.066 Fit side-chains REVERT: A 229 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6578 (pt0) REVERT: A 341 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5256 (mp0) REVERT: B 229 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6585 (pt0) REVERT: B 341 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5256 (mp0) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 1.5992 time to fit residues: 207.3761 Evaluate side-chains 130 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8964 Z= 0.221 Angle : 0.596 7.901 12194 Z= 0.296 Chirality : 0.044 0.146 1220 Planarity : 0.005 0.037 1552 Dihedral : 10.062 113.882 1232 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.62 % Allowed : 11.12 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1048 helix: 0.75 (0.23), residues: 528 sheet: 0.35 (0.58), residues: 70 loop : -1.10 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 430 HIS 0.004 0.001 HIS B 385 PHE 0.013 0.002 PHE A 543 TYR 0.010 0.001 TYR B 326 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.029 Fit side-chains REVERT: A 110 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7386 (p0) REVERT: A 188 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 341 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5277 (mp0) REVERT: B 110 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 188 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 229 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6586 (pt0) REVERT: B 341 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5273 (mp0) outliers start: 15 outliers final: 6 residues processed: 134 average time/residue: 1.5358 time to fit residues: 216.7788 Evaluate side-chains 139 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8964 Z= 0.143 Angle : 0.513 7.162 12194 Z= 0.251 Chirality : 0.041 0.128 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.076 109.453 1232 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.62 % Allowed : 11.34 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1048 helix: 0.98 (0.23), residues: 528 sheet: 0.48 (0.57), residues: 70 loop : -1.00 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.010 0.001 PHE A 543 TYR 0.008 0.001 TYR A 326 ARG 0.001 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.045 Fit side-chains REVERT: A 118 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 188 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 222 LYS cc_start: 0.7285 (mptt) cc_final: 0.6675 (mmmt) REVERT: A 341 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5182 (mp0) REVERT: B 118 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: B 188 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 222 LYS cc_start: 0.7293 (mptt) cc_final: 0.6678 (mmmt) REVERT: B 341 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5189 (mp0) outliers start: 15 outliers final: 4 residues processed: 126 average time/residue: 1.5334 time to fit residues: 204.6370 Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8964 Z= 0.133 Angle : 0.496 6.708 12194 Z= 0.242 Chirality : 0.040 0.125 1220 Planarity : 0.004 0.037 1552 Dihedral : 8.381 106.680 1232 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.30 % Allowed : 11.88 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1048 helix: 1.11 (0.23), residues: 528 sheet: 0.64 (0.58), residues: 70 loop : -0.95 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 430 HIS 0.002 0.001 HIS A 45 PHE 0.009 0.001 PHE A 543 TYR 0.007 0.001 TYR B 326 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.971 Fit side-chains REVERT: A 118 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: A 188 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 222 LYS cc_start: 0.7261 (mptt) cc_final: 0.6644 (ptmm) REVERT: A 254 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (tpp-160) REVERT: A 341 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5167 (mp0) REVERT: B 118 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: B 188 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 222 LYS cc_start: 0.7255 (mptt) cc_final: 0.6662 (ptmm) REVERT: B 254 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (tpp-160) REVERT: B 341 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5242 (mp0) REVERT: B 512 LYS cc_start: 0.7746 (pttp) cc_final: 0.7374 (mmtm) outliers start: 12 outliers final: 4 residues processed: 126 average time/residue: 1.5535 time to fit residues: 206.3227 Evaluate side-chains 134 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8964 Z= 0.142 Angle : 0.508 6.960 12194 Z= 0.249 Chirality : 0.040 0.148 1220 Planarity : 0.004 0.037 1552 Dihedral : 8.347 107.631 1232 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.51 % Allowed : 12.42 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1048 helix: 1.13 (0.23), residues: 528 sheet: 0.72 (0.59), residues: 70 loop : -0.89 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 430 HIS 0.002 0.001 HIS B 45 PHE 0.010 0.001 PHE A 543 TYR 0.008 0.001 TYR B 326 ARG 0.001 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.128 Fit side-chains REVERT: A 118 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: A 152 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7581 (mmtm) REVERT: A 222 LYS cc_start: 0.7245 (mptt) cc_final: 0.6658 (ptmm) REVERT: A 254 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7877 (tpp-160) REVERT: A 341 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5208 (mp0) REVERT: B 118 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 152 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7593 (mmtm) REVERT: B 222 LYS cc_start: 0.7252 (mptt) cc_final: 0.6653 (ptmm) REVERT: B 254 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7869 (tpp-160) REVERT: B 341 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5196 (mp0) outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 1.5449 time to fit residues: 216.8739 Evaluate side-chains 138 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8964 Z= 0.177 Angle : 0.553 7.469 12194 Z= 0.272 Chirality : 0.042 0.159 1220 Planarity : 0.005 0.037 1552 Dihedral : 8.900 112.160 1232 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.62 % Allowed : 12.53 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1048 helix: 1.02 (0.23), residues: 528 sheet: 0.66 (0.59), residues: 70 loop : -0.95 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 430 HIS 0.003 0.001 HIS B 45 PHE 0.010 0.001 PHE B 543 TYR 0.009 0.001 TYR A 326 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.119 Fit side-chains REVERT: A 118 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 188 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 341 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5206 (mp0) REVERT: B 118 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: B 188 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 254 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7844 (tpp-160) REVERT: B 341 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5243 (mp0) outliers start: 15 outliers final: 6 residues processed: 131 average time/residue: 1.5831 time to fit residues: 218.6251 Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8964 Z= 0.226 Angle : 0.618 8.254 12194 Z= 0.306 Chirality : 0.044 0.190 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.909 117.631 1232 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.40 % Allowed : 13.07 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1048 helix: 0.73 (0.23), residues: 540 sheet: 0.63 (0.59), residues: 70 loop : -1.21 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.012 0.002 PHE B 201 TYR 0.010 0.001 TYR B 326 ARG 0.002 0.000 ARG B 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.109 Fit side-chains REVERT: A 118 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 188 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 222 LYS cc_start: 0.7387 (mptt) cc_final: 0.6787 (ptmm) REVERT: A 254 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7857 (tpp-160) REVERT: A 341 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5235 (mp0) REVERT: B 118 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: B 188 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 222 LYS cc_start: 0.7394 (mptt) cc_final: 0.6797 (ptmm) REVERT: B 254 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7851 (tpp-160) REVERT: B 341 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5252 (mp0) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 1.4876 time to fit residues: 202.6227 Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 0.0670 chunk 59 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120794 restraints weight = 8650.011| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.49 r_work: 0.3273 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8964 Z= 0.153 Angle : 0.539 7.521 12194 Z= 0.263 Chirality : 0.041 0.171 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.077 112.833 1232 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.73 % Allowed : 12.63 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1048 helix: 0.86 (0.23), residues: 540 sheet: 0.68 (0.59), residues: 70 loop : -1.13 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 430 HIS 0.002 0.001 HIS B 45 PHE 0.010 0.001 PHE A 543 TYR 0.009 0.001 TYR A 326 ARG 0.001 0.000 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3805.23 seconds wall clock time: 68 minutes 15.34 seconds (4095.34 seconds total)