Starting phenix.real_space_refine on Sun May 11 01:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.map" model { file = "/net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j14_61067/05_2025/9j14_61067.cif" } resolution = 3.49 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= 0.053 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 54 5.16 5 C 4686 2.51 5 N 1160 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7218 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "B" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.31, per 1000 atoms: 0.60 Number of scatterers: 7218 At special positions: 0 Unit cell: (73.7, 115.5, 88, 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 54 16.00 O 1318 8.00 N 1160 7.00 C 4686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.506A pdb=" N HIS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 39 through 55 Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.568A pdb=" N VAL A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.532A pdb=" N CYS A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.250A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.872A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.551A pdb=" N ILE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 3.884A pdb=" N THR A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 4.046A pdb=" N GLY A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.526A pdb=" N LEU B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 39 through 55 Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.569A pdb=" N VAL B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.531A pdb=" N CYS B 77 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.251A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 399 through 406 removed outlier: 3.873A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN B 432 " --> pdb=" O PRO B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.552A pdb=" N ILE B 456 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 3.885A pdb=" N THR B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 479 through 495 removed outlier: 4.045A pdb=" N GLY B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.131A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 394 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.133A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 394 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 221 380 hydrogen bonds defined for protein. 1122 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: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1193 1.33 - 1.45: 1917 1.45 - 1.57: 4164 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 7366 Sorted by residual: bond pdb=" C4 ZEA A 601 " pdb=" C5 ZEA A 601 " ideal model delta sigma weight residual 1.387 1.456 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 ZEA B 601 " pdb=" C5 ZEA B 601 " ideal model delta sigma weight residual 1.387 1.455 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C5 ZEA B 601 " pdb=" C6 ZEA B 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C5 ZEA A 601 " pdb=" C6 ZEA A 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.21e-02 6.83e+03 6.89e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 9893 3.11 - 6.21: 89 6.21 - 9.32: 20 9.32 - 12.43: 2 12.43 - 15.54: 2 Bond angle restraints: 10006 Sorted by residual: angle pdb=" N GLU A 234 " pdb=" CA GLU A 234 " pdb=" C GLU A 234 " ideal model delta sigma weight residual 109.59 94.05 15.54 1.47e+00 4.63e-01 1.12e+02 angle pdb=" N GLU B 234 " pdb=" CA GLU B 234 " pdb=" C GLU B 234 " ideal model delta sigma weight residual 109.59 94.08 15.51 1.47e+00 4.63e-01 1.11e+02 angle pdb=" N THR B 235 " pdb=" CA THR B 235 " pdb=" CB THR B 235 " ideal model delta sigma weight residual 110.77 122.89 -12.12 1.63e+00 3.76e-01 5.53e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" CB THR A 235 " ideal model delta sigma weight residual 110.77 122.81 -12.04 1.63e+00 3.76e-01 5.46e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" C THR A 235 " ideal model delta sigma weight residual 108.26 99.58 8.68 1.66e+00 3.63e-01 2.74e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3681 17.54 - 35.09: 479 35.09 - 52.63: 106 52.63 - 70.18: 12 70.18 - 87.72: 8 Dihedral angle restraints: 4286 sinusoidal: 1558 harmonic: 2728 Sorted by residual: dihedral pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N ALA A 145 " pdb=" CA ALA A 145 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE B 144 " pdb=" C ILE B 144 " pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE B 420 " pdb=" C PHE B 420 " pdb=" N LEU B 421 " pdb=" CA LEU B 421 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 858 0.043 - 0.086: 274 0.086 - 0.129: 59 0.129 - 0.172: 9 0.172 - 0.214: 4 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA GLU B 234 " pdb=" N GLU B 234 " pdb=" C GLU B 234 " pdb=" CB GLU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 234 " pdb=" N GLU A 234 " pdb=" C GLU A 234 " pdb=" CB GLU A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1201 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 439 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 440 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 439 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 440 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 144 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 144 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 144 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 145 " 0.009 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 11 2.32 - 2.96: 3592 2.96 - 3.61: 10586 3.61 - 4.25: 14875 4.25 - 4.90: 26011 Nonbonded interactions: 55075 Sorted by model distance: nonbonded pdb=" CE MET A 450 " pdb=" CH2 TRP B 458 " model vdw 1.674 3.760 nonbonded pdb=" CH2 TRP A 458 " pdb=" CE MET B 450 " model vdw 1.683 3.760 nonbonded pdb=" CE MET A 450 " pdb=" CZ3 TRP B 458 " model vdw 2.133 3.760 nonbonded pdb=" CZ3 TRP A 458 " pdb=" CE MET B 450 " model vdw 2.143 3.760 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.251 3.040 ... (remaining 55070 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: 0.03 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: 0.830 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 0.069 7372 Z= 0.192 Angle : 0.812 15.537 10018 Z= 0.452 Chirality : 0.044 0.214 1204 Planarity : 0.004 0.040 1232 Dihedral : 16.002 87.724 2540 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.26 % Allowed : 27.02 % Favored : 72.72 % 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: -0.73 (0.27), residues: 966 helix: 0.85 (0.23), residues: 572 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 286 HIS 0.003 0.001 HIS A 17 PHE 0.024 0.001 PHE B 295 TYR 0.008 0.001 TYR B 143 ARG 0.004 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.16226 ( 380) hydrogen bonds : angle 5.33571 ( 1122) SS BOND : bond 0.00378 ( 6) SS BOND : angle 1.71785 ( 12) covalent geometry : bond 0.00388 ( 7366) covalent geometry : angle 0.81043 (10006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.809 Fit side-chains REVERT: A 16 LYS cc_start: 0.8466 (tttm) cc_final: 0.7905 (mmmt) REVERT: A 152 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8016 (mtt-85) REVERT: A 184 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6042 (tmtt) REVERT: A 331 LYS cc_start: 0.7062 (mtpp) cc_final: 0.6861 (ptpp) REVERT: A 346 LEU cc_start: 0.8841 (tp) cc_final: 0.8632 (tp) REVERT: A 371 GLU cc_start: 0.7323 (tp30) cc_final: 0.6759 (pt0) REVERT: A 435 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8026 (ptt-90) REVERT: A 448 MET cc_start: 0.7979 (mmm) cc_final: 0.7760 (mmp) REVERT: B 16 LYS cc_start: 0.8462 (tttm) cc_final: 0.7906 (mmmt) REVERT: B 152 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8042 (mtt-85) REVERT: B 184 LYS cc_start: 0.6694 (ttpt) cc_final: 0.5991 (tmtt) REVERT: B 331 LYS cc_start: 0.7011 (mtpp) cc_final: 0.6810 (ptpp) REVERT: B 346 LEU cc_start: 0.8850 (tp) cc_final: 0.8637 (tp) REVERT: B 371 GLU cc_start: 0.7315 (tp30) cc_final: 0.6765 (pt0) REVERT: B 435 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8131 (ptt-90) REVERT: B 448 MET cc_start: 0.8021 (mmm) cc_final: 0.7814 (mmp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.1927 time to fit residues: 41.1230 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 211 GLN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145782 restraints weight = 9266.290| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.45 r_work: 0.3473 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7372 Z= 0.138 Angle : 0.608 6.384 10018 Z= 0.321 Chirality : 0.043 0.167 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.893 29.231 1030 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 6.66 % Allowed : 21.93 % Favored : 71.41 % 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: -0.49 (0.27), residues: 966 helix: 1.10 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.57 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 458 HIS 0.002 0.001 HIS B 17 PHE 0.010 0.001 PHE A 207 TYR 0.012 0.001 TYR A 143 ARG 0.003 0.000 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 380) hydrogen bonds : angle 4.12628 ( 1122) SS BOND : bond 0.00161 ( 6) SS BOND : angle 2.12570 ( 12) covalent geometry : bond 0.00322 ( 7366) covalent geometry : angle 0.60426 (10006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8378 (tttm) cc_final: 0.7884 (mmmt) REVERT: A 33 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7258 (mt) REVERT: A 104 ARG cc_start: 0.7364 (ttp-110) cc_final: 0.6899 (mtm180) REVERT: A 124 MET cc_start: 0.8645 (tpt) cc_final: 0.8108 (tpp) REVERT: A 138 MET cc_start: 0.8890 (mmm) cc_final: 0.7751 (mmt) REVERT: A 152 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8357 (mtt-85) REVERT: A 171 CYS cc_start: 0.8483 (m) cc_final: 0.8058 (t) REVERT: A 184 LYS cc_start: 0.7085 (ttpt) cc_final: 0.5957 (tmtt) REVERT: A 234 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6927 (tp30) REVERT: A 330 ARG cc_start: 0.3850 (mpt180) cc_final: 0.2840 (tmm160) REVERT: A 371 GLU cc_start: 0.7057 (tp30) cc_final: 0.6810 (pt0) REVERT: A 448 MET cc_start: 0.8627 (mmm) cc_final: 0.8147 (mmp) REVERT: A 450 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8650 (tmm) REVERT: A 460 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: B 16 LYS cc_start: 0.8424 (tttm) cc_final: 0.7926 (mmmt) REVERT: B 33 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 104 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.6895 (mtm180) REVERT: B 124 MET cc_start: 0.8643 (tpt) cc_final: 0.8097 (tpp) REVERT: B 138 MET cc_start: 0.8889 (mmm) cc_final: 0.7759 (mmt) REVERT: B 152 ARG cc_start: 0.8731 (mtt180) cc_final: 0.8345 (mtt-85) REVERT: B 171 CYS cc_start: 0.8494 (m) cc_final: 0.8060 (t) REVERT: B 184 LYS cc_start: 0.7090 (ttpt) cc_final: 0.5960 (tmtt) REVERT: B 226 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 234 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6914 (tp30) REVERT: B 330 ARG cc_start: 0.4383 (mpt180) cc_final: 0.3125 (tmm160) REVERT: B 356 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6305 (tpt) REVERT: B 371 GLU cc_start: 0.7046 (tp30) cc_final: 0.6742 (pt0) REVERT: B 448 MET cc_start: 0.8617 (mmm) cc_final: 0.8123 (mmp) REVERT: B 450 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: B 460 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7832 (mt-10) outliers start: 51 outliers final: 23 residues processed: 181 average time/residue: 0.2277 time to fit residues: 52.4482 Evaluate side-chains 154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143619 restraints weight = 9321.394| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.43 r_work: 0.3425 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7372 Z= 0.139 Angle : 0.605 5.629 10018 Z= 0.317 Chirality : 0.043 0.198 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.867 30.735 1030 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 7.05 % Allowed : 21.93 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.35 (0.27), residues: 966 helix: 1.27 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 458 HIS 0.003 0.001 HIS B 17 PHE 0.009 0.001 PHE B 368 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 380) hydrogen bonds : angle 4.10632 ( 1122) SS BOND : bond 0.00125 ( 6) SS BOND : angle 2.10985 ( 12) covalent geometry : bond 0.00328 ( 7366) covalent geometry : angle 0.60139 (10006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8453 (tttm) cc_final: 0.7988 (mmmt) REVERT: A 33 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 94 SER cc_start: 0.8808 (m) cc_final: 0.8582 (p) REVERT: A 104 ARG cc_start: 0.7371 (ttp-110) cc_final: 0.6747 (mtm180) REVERT: A 124 MET cc_start: 0.8713 (tpt) cc_final: 0.8171 (tpp) REVERT: A 152 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8362 (mtt-85) REVERT: A 179 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7420 (pp) REVERT: A 184 LYS cc_start: 0.7045 (ttpt) cc_final: 0.5892 (tmtt) REVERT: A 234 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7344 (tp30) REVERT: A 330 ARG cc_start: 0.4610 (mpt180) cc_final: 0.3287 (ttp-170) REVERT: A 435 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8138 (ptt-90) REVERT: A 448 MET cc_start: 0.8594 (mmm) cc_final: 0.8389 (mmm) REVERT: A 450 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: A 460 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: A 463 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 16 LYS cc_start: 0.8461 (tttm) cc_final: 0.7984 (mmmt) REVERT: B 33 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7519 (mt) REVERT: B 76 ASP cc_start: 0.8329 (m-30) cc_final: 0.8126 (m-30) REVERT: B 94 SER cc_start: 0.8818 (m) cc_final: 0.8582 (p) REVERT: B 104 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.6732 (mtm180) REVERT: B 124 MET cc_start: 0.8713 (tpt) cc_final: 0.8167 (tpp) REVERT: B 152 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8296 (mtt-85) REVERT: B 179 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7430 (pp) REVERT: B 184 LYS cc_start: 0.7060 (ttpt) cc_final: 0.5897 (tmtt) REVERT: B 234 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7287 (tp30) REVERT: B 330 ARG cc_start: 0.4599 (mpt180) cc_final: 0.3272 (ttp-170) REVERT: B 435 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8128 (ptt-90) REVERT: B 448 MET cc_start: 0.8655 (mmm) cc_final: 0.8440 (mmm) REVERT: B 450 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: B 460 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: B 463 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8271 (mm-30) outliers start: 54 outliers final: 32 residues processed: 176 average time/residue: 0.1936 time to fit residues: 44.9522 Evaluate side-chains 168 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145330 restraints weight = 9363.007| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.46 r_work: 0.3438 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7372 Z= 0.116 Angle : 0.567 6.065 10018 Z= 0.299 Chirality : 0.041 0.231 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.682 30.416 1030 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.87 % Allowed : 21.28 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.24 (0.28), residues: 966 helix: 1.24 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 253 HIS 0.003 0.001 HIS B 17 PHE 0.008 0.001 PHE A 51 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 380) hydrogen bonds : angle 4.02993 ( 1122) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.71362 ( 12) covalent geometry : bond 0.00267 ( 7366) covalent geometry : angle 0.56449 (10006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8404 (tttm) cc_final: 0.7935 (mmmt) REVERT: A 94 SER cc_start: 0.8803 (m) cc_final: 0.8582 (p) REVERT: A 124 MET cc_start: 0.8663 (tpt) cc_final: 0.8117 (tpp) REVERT: A 152 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8228 (mtt-85) REVERT: A 179 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7414 (pp) REVERT: A 184 LYS cc_start: 0.6964 (ttpt) cc_final: 0.5788 (tmtt) REVERT: A 234 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7598 (tm-30) REVERT: A 330 ARG cc_start: 0.4559 (mpt180) cc_final: 0.3255 (ttp-170) REVERT: A 448 MET cc_start: 0.8585 (mmm) cc_final: 0.8376 (mmm) REVERT: B 16 LYS cc_start: 0.8406 (tttm) cc_final: 0.7941 (mmmt) REVERT: B 94 SER cc_start: 0.8801 (m) cc_final: 0.8583 (p) REVERT: B 104 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6830 (mtm180) REVERT: B 124 MET cc_start: 0.8664 (tpt) cc_final: 0.8118 (tpp) REVERT: B 152 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8211 (mtt-85) REVERT: B 179 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7418 (pp) REVERT: B 184 LYS cc_start: 0.6944 (ttpt) cc_final: 0.5755 (tmtt) REVERT: B 234 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7594 (tm-30) REVERT: B 330 ARG cc_start: 0.4533 (mpt180) cc_final: 0.3247 (ttp-170) REVERT: B 448 MET cc_start: 0.8593 (mmm) cc_final: 0.8381 (mmm) REVERT: B 460 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7732 (mt-10) outliers start: 45 outliers final: 24 residues processed: 153 average time/residue: 0.1735 time to fit residues: 36.3587 Evaluate side-chains 144 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.0030 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145499 restraints weight = 9337.294| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.46 r_work: 0.3449 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7372 Z= 0.114 Angle : 0.564 6.050 10018 Z= 0.297 Chirality : 0.041 0.251 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.619 30.536 1030 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 6.14 % Allowed : 20.37 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.27), residues: 966 helix: 1.30 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -2.42 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 PHE 0.008 0.001 PHE B 51 TYR 0.010 0.001 TYR A 343 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 380) hydrogen bonds : angle 3.96367 ( 1122) SS BOND : bond 0.00583 ( 6) SS BOND : angle 1.42831 ( 12) covalent geometry : bond 0.00261 ( 7366) covalent geometry : angle 0.56181 (10006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8326 (tttm) cc_final: 0.7892 (mmmt) REVERT: A 94 SER cc_start: 0.8787 (m) cc_final: 0.8583 (p) REVERT: A 124 MET cc_start: 0.8630 (tpt) cc_final: 0.8117 (tpp) REVERT: A 179 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7398 (pp) REVERT: A 182 ARG cc_start: 0.7296 (ttp80) cc_final: 0.7095 (ttp80) REVERT: A 184 LYS cc_start: 0.6901 (ttpt) cc_final: 0.5747 (tmtt) REVERT: A 328 GLU cc_start: 0.7992 (tp30) cc_final: 0.7748 (tp30) REVERT: A 330 ARG cc_start: 0.4483 (mpt180) cc_final: 0.3296 (ttp-170) REVERT: B 16 LYS cc_start: 0.8344 (tttm) cc_final: 0.7905 (mmmt) REVERT: B 94 SER cc_start: 0.8774 (m) cc_final: 0.8572 (p) REVERT: B 124 MET cc_start: 0.8614 (tpt) cc_final: 0.8095 (tpp) REVERT: B 179 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7440 (pp) REVERT: B 182 ARG cc_start: 0.7303 (ttp80) cc_final: 0.7103 (ttp80) REVERT: B 184 LYS cc_start: 0.6885 (ttpt) cc_final: 0.5726 (tmtt) REVERT: B 330 ARG cc_start: 0.4452 (mpt180) cc_final: 0.3259 (ttp-170) REVERT: B 460 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7657 (mt-10) outliers start: 47 outliers final: 26 residues processed: 159 average time/residue: 0.1576 time to fit residues: 35.2035 Evaluate side-chains 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 80 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142960 restraints weight = 9442.352| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.45 r_work: 0.3411 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7372 Z= 0.135 Angle : 0.589 6.261 10018 Z= 0.308 Chirality : 0.042 0.267 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.719 30.105 1030 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 5.87 % Allowed : 19.97 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.28), residues: 966 helix: 1.21 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.002 0.001 HIS A 17 PHE 0.008 0.001 PHE A 51 TYR 0.009 0.001 TYR A 343 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 380) hydrogen bonds : angle 3.96388 ( 1122) SS BOND : bond 0.00551 ( 6) SS BOND : angle 2.15963 ( 12) covalent geometry : bond 0.00322 ( 7366) covalent geometry : angle 0.58426 (10006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8331 (tttm) cc_final: 0.7885 (mmmt) REVERT: A 33 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 94 SER cc_start: 0.8792 (m) cc_final: 0.8577 (p) REVERT: A 124 MET cc_start: 0.8693 (tpt) cc_final: 0.8183 (tpp) REVERT: A 179 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7441 (pp) REVERT: A 184 LYS cc_start: 0.6855 (ttpt) cc_final: 0.5675 (tmtt) REVERT: A 328 GLU cc_start: 0.7881 (tp30) cc_final: 0.7582 (mt-10) REVERT: A 330 ARG cc_start: 0.4541 (mpt180) cc_final: 0.3295 (ttp-170) REVERT: A 448 MET cc_start: 0.8499 (mmm) cc_final: 0.8149 (mmp) REVERT: B 16 LYS cc_start: 0.8339 (tttm) cc_final: 0.7889 (mmmt) REVERT: B 33 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 76 ASP cc_start: 0.8432 (m-30) cc_final: 0.8092 (t0) REVERT: B 94 SER cc_start: 0.8787 (m) cc_final: 0.8560 (p) REVERT: B 124 MET cc_start: 0.8670 (tpt) cc_final: 0.8126 (tpp) REVERT: B 179 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7467 (pp) REVERT: B 184 LYS cc_start: 0.6845 (ttpt) cc_final: 0.5673 (tmtt) REVERT: B 328 GLU cc_start: 0.7873 (tp30) cc_final: 0.7578 (mt-10) REVERT: B 330 ARG cc_start: 0.4517 (mpt180) cc_final: 0.3279 (ttp-170) REVERT: B 448 MET cc_start: 0.8529 (mmm) cc_final: 0.8178 (mmp) REVERT: B 460 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7638 (mt-10) outliers start: 45 outliers final: 34 residues processed: 146 average time/residue: 0.1666 time to fit residues: 34.1397 Evaluate side-chains 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN B 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.179149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147317 restraints weight = 9333.473| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.45 r_work: 0.3473 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7372 Z= 0.105 Angle : 0.564 6.502 10018 Z= 0.295 Chirality : 0.041 0.244 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.533 30.548 1030 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 5.09 % Allowed : 21.02 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.28), residues: 966 helix: 1.41 (0.22), residues: 578 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 PHE 0.006 0.001 PHE B 51 TYR 0.010 0.001 TYR A 375 ARG 0.004 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 380) hydrogen bonds : angle 3.90574 ( 1122) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.66240 ( 12) covalent geometry : bond 0.00234 ( 7366) covalent geometry : angle 0.56165 (10006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8306 (tttm) cc_final: 0.7873 (mmmt) REVERT: A 124 MET cc_start: 0.8622 (tpt) cc_final: 0.8073 (tpp) REVERT: A 152 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8200 (mtt-85) REVERT: A 179 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7386 (pp) REVERT: A 328 GLU cc_start: 0.7931 (tp30) cc_final: 0.7569 (mt-10) REVERT: A 330 ARG cc_start: 0.4382 (mpt180) cc_final: 0.3300 (ttp-170) REVERT: A 448 MET cc_start: 0.8453 (mmm) cc_final: 0.8094 (mmp) REVERT: B 16 LYS cc_start: 0.8313 (tttm) cc_final: 0.7882 (mmmt) REVERT: B 124 MET cc_start: 0.8606 (tpt) cc_final: 0.8057 (tpp) REVERT: B 152 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8185 (mtt-85) REVERT: B 179 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7396 (pp) REVERT: B 328 GLU cc_start: 0.7924 (tp30) cc_final: 0.7560 (mt-10) REVERT: B 330 ARG cc_start: 0.4373 (mpt180) cc_final: 0.3298 (ttp-170) REVERT: B 448 MET cc_start: 0.8483 (mmm) cc_final: 0.8127 (mmp) outliers start: 39 outliers final: 26 residues processed: 143 average time/residue: 0.1796 time to fit residues: 34.7832 Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145650 restraints weight = 9512.197| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.46 r_work: 0.3343 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7372 Z= 0.119 Angle : 0.575 6.647 10018 Z= 0.302 Chirality : 0.041 0.269 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.550 30.239 1030 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 4.70 % Allowed : 22.06 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.16 (0.28), residues: 966 helix: 1.34 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 PHE 0.008 0.001 PHE B 51 TYR 0.025 0.001 TYR A 375 ARG 0.010 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 380) hydrogen bonds : angle 3.89393 ( 1122) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.45617 ( 12) covalent geometry : bond 0.00276 ( 7366) covalent geometry : angle 0.57323 (10006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8316 (tttm) cc_final: 0.7835 (mmmt) REVERT: A 33 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7356 (mt) REVERT: A 179 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7435 (pp) REVERT: A 328 GLU cc_start: 0.8209 (tp30) cc_final: 0.7689 (mt-10) REVERT: A 330 ARG cc_start: 0.4562 (mpt180) cc_final: 0.3160 (ttp-170) REVERT: A 448 MET cc_start: 0.8587 (mmm) cc_final: 0.8210 (mmp) REVERT: B 16 LYS cc_start: 0.8321 (tttm) cc_final: 0.7842 (mmmt) REVERT: B 33 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7345 (mt) REVERT: B 124 MET cc_start: 0.8704 (tpt) cc_final: 0.8124 (tpp) REVERT: B 152 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8266 (mtt-85) REVERT: B 179 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7429 (pp) REVERT: B 328 GLU cc_start: 0.8165 (tp30) cc_final: 0.7656 (mt-10) REVERT: B 330 ARG cc_start: 0.4525 (mpt180) cc_final: 0.3143 (ttp-170) REVERT: B 448 MET cc_start: 0.8689 (mmm) cc_final: 0.8309 (mmp) outliers start: 36 outliers final: 24 residues processed: 137 average time/residue: 0.1629 time to fit residues: 30.8919 Evaluate side-chains 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145197 restraints weight = 9412.620| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.43 r_work: 0.3436 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7372 Z= 0.128 Angle : 0.602 8.614 10018 Z= 0.317 Chirality : 0.042 0.246 1204 Planarity : 0.005 0.070 1232 Dihedral : 4.619 30.304 1030 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.79 % Allowed : 23.24 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.16 (0.28), residues: 966 helix: 1.34 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.52 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 458 HIS 0.002 0.001 HIS A 17 PHE 0.008 0.001 PHE A 51 TYR 0.020 0.001 TYR B 375 ARG 0.001 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 380) hydrogen bonds : angle 3.90805 ( 1122) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.44561 ( 12) covalent geometry : bond 0.00297 ( 7366) covalent geometry : angle 0.60040 (10006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8314 (tttm) cc_final: 0.7886 (mmmt) REVERT: A 33 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7381 (mt) REVERT: A 179 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7382 (pp) REVERT: A 328 GLU cc_start: 0.7931 (tp30) cc_final: 0.7558 (mt-10) REVERT: A 330 ARG cc_start: 0.4465 (mpt180) cc_final: 0.3297 (ttp-170) REVERT: A 448 MET cc_start: 0.8384 (mmm) cc_final: 0.8042 (mmp) REVERT: B 16 LYS cc_start: 0.8345 (tttm) cc_final: 0.7914 (mmmt) REVERT: B 33 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 124 MET cc_start: 0.8626 (tpt) cc_final: 0.8027 (tpp) REVERT: B 152 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8182 (mtt-85) REVERT: B 179 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7416 (pp) REVERT: B 328 GLU cc_start: 0.7938 (tp30) cc_final: 0.7567 (mt-10) REVERT: B 330 ARG cc_start: 0.4451 (mpt180) cc_final: 0.3280 (ttp-170) REVERT: B 448 MET cc_start: 0.8469 (mmm) cc_final: 0.8083 (mmp) outliers start: 29 outliers final: 24 residues processed: 121 average time/residue: 0.1765 time to fit residues: 29.5685 Evaluate side-chains 118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 44 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.178769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146895 restraints weight = 9489.975| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.46 r_work: 0.3465 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7372 Z= 0.111 Angle : 0.571 8.174 10018 Z= 0.298 Chirality : 0.041 0.237 1204 Planarity : 0.005 0.079 1232 Dihedral : 4.527 30.490 1030 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 3.79 % Allowed : 22.98 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.14 (0.28), residues: 966 helix: 1.35 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.51 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 458 HIS 0.003 0.001 HIS A 17 PHE 0.007 0.001 PHE B 31 TYR 0.016 0.001 TYR B 375 ARG 0.005 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 380) hydrogen bonds : angle 3.88177 ( 1122) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.23192 ( 12) covalent geometry : bond 0.00251 ( 7366) covalent geometry : angle 0.56946 (10006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8304 (tttm) cc_final: 0.7890 (mmmt) REVERT: A 33 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7358 (mt) REVERT: A 152 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8194 (mtt-85) REVERT: A 179 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7459 (pp) REVERT: A 328 GLU cc_start: 0.7887 (tp30) cc_final: 0.7545 (mt-10) REVERT: A 330 ARG cc_start: 0.4391 (mpt180) cc_final: 0.3307 (ttp-170) REVERT: A 448 MET cc_start: 0.8382 (mmm) cc_final: 0.8020 (mmp) REVERT: B 16 LYS cc_start: 0.8327 (tttm) cc_final: 0.7919 (mmmt) REVERT: B 33 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7355 (mt) REVERT: B 152 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8180 (mtt-85) REVERT: B 179 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7392 (pp) REVERT: B 328 GLU cc_start: 0.7903 (tp30) cc_final: 0.7536 (mt-10) REVERT: B 330 ARG cc_start: 0.4318 (mpt180) cc_final: 0.3276 (ttp-170) REVERT: B 448 MET cc_start: 0.8381 (mmm) cc_final: 0.8020 (mmp) outliers start: 29 outliers final: 21 residues processed: 120 average time/residue: 0.1637 time to fit residues: 27.4726 Evaluate side-chains 118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141291 restraints weight = 9555.195| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.47 r_work: 0.3424 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7372 Z= 0.108 Angle : 0.571 8.114 10018 Z= 0.296 Chirality : 0.041 0.233 1204 Planarity : 0.005 0.070 1232 Dihedral : 4.446 30.235 1030 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.92 % Allowed : 22.45 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.09 (0.28), residues: 966 helix: 1.38 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.48 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 458 HIS 0.003 0.001 HIS B 17 PHE 0.006 0.001 PHE B 51 TYR 0.011 0.001 TYR B 375 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 380) hydrogen bonds : angle 3.86324 ( 1122) SS BOND : bond 0.00229 ( 6) SS BOND : angle 1.20313 ( 12) covalent geometry : bond 0.00242 ( 7366) covalent geometry : angle 0.56935 (10006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.29 seconds wall clock time: 51 minutes 58.33 seconds (3118.33 seconds total)