Starting phenix.real_space_refine on Mon Apr 28 08:13:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j14_61067/04_2025/9j14_61067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j14_61067/04_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_61067/04_2025/9j14_61067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j14_61067/04_2025/9j14_61067.map" model { file = "/net/cci-nas-00/data/ceres_data/9j14_61067/04_2025/9j14_61067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j14_61067/04_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-5669/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: 4.73, per 1000 atoms: 0.66 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 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: 0.92 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: 2.74 Time building geometry restraints manager: 2.35 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: 0.05 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: 0.840 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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 : 0.639 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: 0.2079 time to fit residues: 44.1889 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 : 0.746 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145778 restraints weight = 9266.294| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.45 r_work: 0.3431 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 2.12574 ( 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 : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8374 (tttm) cc_final: 0.7879 (mmmt) REVERT: A 33 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7248 (mt) REVERT: A 104 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.6892 (mtm180) REVERT: A 124 MET cc_start: 0.8643 (tpt) cc_final: 0.8104 (tpp) REVERT: A 138 MET cc_start: 0.8884 (mmm) cc_final: 0.7749 (mmt) REVERT: A 152 ARG cc_start: 0.8731 (mtt180) cc_final: 0.8346 (mtt-85) REVERT: A 171 CYS cc_start: 0.8460 (m) cc_final: 0.8043 (t) REVERT: A 184 LYS cc_start: 0.7084 (ttpt) cc_final: 0.5957 (tmtt) REVERT: A 234 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6916 (tp30) REVERT: A 330 ARG cc_start: 0.3838 (mpt180) cc_final: 0.2832 (tmm160) REVERT: A 371 GLU cc_start: 0.7052 (tp30) cc_final: 0.6800 (pt0) REVERT: A 448 MET cc_start: 0.8632 (mmm) cc_final: 0.8152 (mmp) REVERT: A 450 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: A 460 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: B 16 LYS cc_start: 0.8421 (tttm) cc_final: 0.7924 (mmmt) REVERT: B 33 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7266 (mt) REVERT: B 104 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.6890 (mtm180) REVERT: B 124 MET cc_start: 0.8641 (tpt) cc_final: 0.8095 (tpp) REVERT: B 138 MET cc_start: 0.8887 (mmm) cc_final: 0.7761 (mmt) REVERT: B 152 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8337 (mtt-85) REVERT: B 171 CYS cc_start: 0.8469 (m) cc_final: 0.8041 (t) REVERT: B 184 LYS cc_start: 0.7084 (ttpt) cc_final: 0.5956 (tmtt) REVERT: B 226 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8627 (mt) REVERT: B 234 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6901 (tp30) REVERT: B 330 ARG cc_start: 0.4371 (mpt180) cc_final: 0.3112 (tmm160) REVERT: B 356 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6294 (tpt) REVERT: B 371 GLU cc_start: 0.7045 (tp30) cc_final: 0.6728 (pt0) REVERT: B 448 MET cc_start: 0.8625 (mmm) cc_final: 0.8130 (mmp) REVERT: B 450 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8659 (tmm) REVERT: B 460 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 51 outliers final: 23 residues processed: 181 average time/residue: 0.2369 time to fit residues: 54.6696 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 : 0.835 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.177460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145721 restraints weight = 9301.460| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.42 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2358 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= 0.123 Angle : 0.590 5.544 10018 Z= 0.308 Chirality : 0.042 0.194 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.792 30.829 1030 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 5.74 % Allowed : 23.24 % 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: -0.31 (0.27), residues: 966 helix: 1.30 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.59 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 458 HIS 0.003 0.001 HIS B 17 PHE 0.010 0.001 PHE B 368 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 380) hydrogen bonds : angle 4.06353 ( 1122) SS BOND : bond 0.00140 ( 6) SS BOND : angle 2.16552 ( 12) covalent geometry : bond 0.00286 ( 7366) covalent geometry : angle 0.58582 (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 181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.760 Fit side-chains REVERT: A 16 LYS cc_start: 0.8387 (tttm) cc_final: 0.7866 (mmmt) REVERT: A 94 SER cc_start: 0.8845 (m) cc_final: 0.8607 (p) REVERT: A 104 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.6875 (mtm180) REVERT: A 124 MET cc_start: 0.8764 (tpt) cc_final: 0.8205 (tpp) REVERT: A 152 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 171 CYS cc_start: 0.8692 (m) cc_final: 0.8145 (t) REVERT: A 179 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7370 (pp) REVERT: A 184 LYS cc_start: 0.6990 (ttpt) cc_final: 0.5766 (tmtt) REVERT: A 234 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7310 (tp30) REVERT: A 330 ARG cc_start: 0.4636 (mpt180) cc_final: 0.3084 (ttp-170) REVERT: A 362 PHE cc_start: 0.6732 (m-10) cc_final: 0.6529 (m-10) REVERT: A 371 GLU cc_start: 0.7088 (tp30) cc_final: 0.6819 (pt0) REVERT: A 435 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8225 (ptt-90) REVERT: A 448 MET cc_start: 0.8752 (mmm) cc_final: 0.8542 (mmm) REVERT: A 450 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (tmm) REVERT: A 460 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: B 16 LYS cc_start: 0.8465 (tttm) cc_final: 0.7928 (mmmt) REVERT: B 94 SER cc_start: 0.8850 (m) cc_final: 0.8602 (p) REVERT: B 104 ARG cc_start: 0.7515 (ttp-110) cc_final: 0.6895 (mtm180) REVERT: B 124 MET cc_start: 0.8767 (tpt) cc_final: 0.8204 (tpp) REVERT: B 152 ARG cc_start: 0.8731 (mtt180) cc_final: 0.8339 (mtt-85) REVERT: B 171 CYS cc_start: 0.8654 (m) cc_final: 0.8138 (t) REVERT: B 179 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7352 (pp) REVERT: B 184 LYS cc_start: 0.6998 (ttpt) cc_final: 0.5761 (tmtt) REVERT: B 234 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7308 (tp30) REVERT: B 330 ARG cc_start: 0.4612 (mpt180) cc_final: 0.3074 (ttp-170) REVERT: B 362 PHE cc_start: 0.6812 (m-10) cc_final: 0.6595 (m-10) REVERT: B 371 GLU cc_start: 0.7080 (tp30) cc_final: 0.6827 (pt0) REVERT: B 435 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8212 (ptt-90) REVERT: B 448 MET cc_start: 0.8736 (mmm) cc_final: 0.8525 (mmm) REVERT: B 450 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8823 (tmm) REVERT: B 460 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7987 (mt-10) outliers start: 44 outliers final: 22 residues processed: 166 average time/residue: 0.2005 time to fit residues: 43.6321 Evaluate side-chains 149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR 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 279 VAL Chi-restraints excluded: chain A residue 285 SER 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 38 THR 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 279 VAL 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 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: 0.5980 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.175816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144054 restraints weight = 9398.243| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.46 r_work: 0.3428 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7372 Z= 0.126 Angle : 0.574 6.141 10018 Z= 0.303 Chirality : 0.042 0.231 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.705 30.140 1030 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 8.09 % Allowed : 19.97 % Favored : 71.93 % 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: -0.23 (0.28), residues: 966 helix: 1.23 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -2.46 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.003 0.001 HIS B 17 PHE 0.008 0.001 PHE B 51 TYR 0.011 0.001 TYR A 143 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 380) hydrogen bonds : angle 4.03763 ( 1122) SS BOND : bond 0.00178 ( 6) SS BOND : angle 1.66762 ( 12) covalent geometry : bond 0.00295 ( 7366) covalent geometry : angle 0.57151 (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 194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 0.706 Fit side-chains REVERT: A 16 LYS cc_start: 0.8368 (tttm) cc_final: 0.7929 (mmmt) REVERT: A 33 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 94 SER cc_start: 0.8805 (m) cc_final: 0.8587 (p) REVERT: A 104 ARG cc_start: 0.7326 (ttp-110) cc_final: 0.6825 (mtm180) REVERT: A 124 MET cc_start: 0.8706 (tpt) cc_final: 0.8160 (tpp) REVERT: A 152 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8238 (mtt-85) REVERT: A 179 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7463 (pp) REVERT: A 184 LYS cc_start: 0.6942 (ttpt) cc_final: 0.5768 (tmtt) REVERT: A 330 ARG cc_start: 0.4588 (mpt180) cc_final: 0.3313 (ttp-170) REVERT: A 448 MET cc_start: 0.8626 (mmm) cc_final: 0.8408 (mmm) REVERT: A 460 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 16 LYS cc_start: 0.8406 (tttm) cc_final: 0.7945 (mmmt) REVERT: B 33 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 76 ASP cc_start: 0.8446 (m-30) cc_final: 0.8225 (m-30) REVERT: B 94 SER cc_start: 0.8803 (m) cc_final: 0.8588 (p) REVERT: B 104 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.6831 (mtm180) REVERT: B 124 MET cc_start: 0.8702 (tpt) cc_final: 0.8156 (tpp) REVERT: B 152 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8219 (mtt-85) REVERT: B 156 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7580 (t) REVERT: B 179 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7463 (pp) REVERT: B 184 LYS cc_start: 0.6953 (ttpt) cc_final: 0.5780 (tmtt) REVERT: B 222 ASP cc_start: 0.8659 (t70) cc_final: 0.8429 (t0) REVERT: B 234 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7601 (tm-30) REVERT: B 330 ARG cc_start: 0.4566 (mpt180) cc_final: 0.3297 (ttp-170) REVERT: B 448 MET cc_start: 0.8628 (mmm) cc_final: 0.8408 (mmm) REVERT: B 460 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7724 (mt-10) outliers start: 62 outliers final: 36 residues processed: 175 average time/residue: 0.1759 time to fit residues: 41.9310 Evaluate side-chains 155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 109 LEU 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 290 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 THR 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 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 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 156 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 219 VAL 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 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: 0.2980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.0370 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.180908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149237 restraints weight = 9377.844| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.44 r_work: 0.3259 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7372 Z= 0.104 Angle : 0.557 5.933 10018 Z= 0.293 Chirality : 0.041 0.248 1204 Planarity : 0.004 0.044 1232 Dihedral : 4.557 30.977 1030 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 5.61 % Allowed : 21.41 % 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: -0.17 (0.27), residues: 966 helix: 1.25 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 372 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 0.006 0.001 PHE B 51 TYR 0.009 0.001 TYR B 343 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 380) hydrogen bonds : angle 3.95814 ( 1122) SS BOND : bond 0.00528 ( 6) SS BOND : angle 1.57344 ( 12) covalent geometry : bond 0.00226 ( 7366) covalent geometry : angle 0.55501 (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 165 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.717 Fit side-chains REVERT: A 16 LYS cc_start: 0.8339 (tttm) cc_final: 0.7835 (mmmt) REVERT: A 33 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7267 (mt) REVERT: A 94 SER cc_start: 0.8820 (m) cc_final: 0.8598 (p) REVERT: A 104 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.6795 (mtm180) REVERT: A 124 MET cc_start: 0.8682 (tpt) cc_final: 0.8125 (tpp) REVERT: A 152 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8243 (mtt-85) REVERT: A 179 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7419 (pp) REVERT: A 330 ARG cc_start: 0.4432 (mpt180) cc_final: 0.3033 (ttp-170) REVERT: A 435 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8180 (ptt-90) REVERT: B 16 LYS cc_start: 0.8340 (tttm) cc_final: 0.7842 (mmmt) REVERT: B 33 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7260 (mt) REVERT: B 94 SER cc_start: 0.8819 (m) cc_final: 0.8594 (p) REVERT: B 104 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.6776 (mtm180) REVERT: B 124 MET cc_start: 0.8681 (tpt) cc_final: 0.8124 (tpp) REVERT: B 152 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8229 (mtt-85) REVERT: B 179 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7436 (pp) REVERT: B 234 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7476 (tm-30) REVERT: B 330 ARG cc_start: 0.4343 (mpt180) cc_final: 0.3039 (ttp-170) REVERT: B 435 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8176 (ptt-90) outliers start: 43 outliers final: 29 residues processed: 153 average time/residue: 0.1878 time to fit residues: 38.4664 Evaluate side-chains 149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 109 LEU 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 279 VAL Chi-restraints excluded: chain A residue 285 SER 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 33 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.178720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146496 restraints weight = 9488.742| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.46 r_work: 0.3459 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7372 Z= 0.119 Angle : 0.589 6.381 10018 Z= 0.306 Chirality : 0.041 0.262 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.613 30.287 1030 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 5.35 % Allowed : 21.80 % 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: -0.17 (0.27), residues: 966 helix: 1.30 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -2.49 (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 A 51 TYR 0.021 0.001 TYR B 375 ARG 0.013 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 380) hydrogen bonds : angle 3.94528 ( 1122) SS BOND : bond 0.00369 ( 6) SS BOND : angle 2.53894 ( 12) covalent geometry : bond 0.00278 ( 7366) covalent geometry : angle 0.58257 (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 157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.710 Fit side-chains REVERT: A 16 LYS cc_start: 0.8327 (tttm) cc_final: 0.7882 (mmmt) REVERT: A 33 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7414 (mt) REVERT: A 94 SER cc_start: 0.8780 (m) cc_final: 0.8566 (p) REVERT: A 104 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7105 (mtp85) REVERT: A 179 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7449 (pp) REVERT: A 234 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 328 GLU cc_start: 0.8097 (tp30) cc_final: 0.7556 (tp30) REVERT: A 330 ARG cc_start: 0.4442 (mpt180) cc_final: 0.3289 (ttp-170) REVERT: A 448 MET cc_start: 0.8458 (mmm) cc_final: 0.8111 (mmp) REVERT: B 16 LYS cc_start: 0.8325 (tttm) cc_final: 0.7884 (mmmt) REVERT: B 33 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7408 (mt) REVERT: B 104 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7081 (mtp85) REVERT: B 152 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8188 (mtt-85) REVERT: B 179 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7421 (pp) REVERT: B 328 GLU cc_start: 0.8110 (tp30) cc_final: 0.7572 (tp30) REVERT: B 330 ARG cc_start: 0.4430 (mpt180) cc_final: 0.3273 (ttp-170) REVERT: B 448 MET cc_start: 0.8487 (mmm) cc_final: 0.8139 (mmp) outliers start: 41 outliers final: 28 residues processed: 148 average time/residue: 0.2043 time to fit residues: 41.3125 Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 109 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 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 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 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 88 optimal weight: 0.0980 chunk 32 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.173590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142357 restraints weight = 9554.979| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.43 r_work: 0.3436 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7372 Z= 0.106 Angle : 0.573 6.998 10018 Z= 0.299 Chirality : 0.041 0.243 1204 Planarity : 0.005 0.062 1232 Dihedral : 4.479 30.440 1030 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 4.57 % Allowed : 22.32 % Favored : 73.11 % 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 (0.27), residues: 966 helix: 1.42 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -2.55 (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 0.006 0.001 PHE A 51 TYR 0.015 0.001 TYR B 375 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 380) hydrogen bonds : angle 3.89968 ( 1122) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.88863 ( 12) covalent geometry : bond 0.00238 ( 7366) covalent geometry : angle 0.56941 (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 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.836 Fit side-chains REVERT: A 16 LYS cc_start: 0.8299 (tttm) cc_final: 0.7807 (mmmt) REVERT: A 33 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7298 (mt) REVERT: A 76 ASP cc_start: 0.8499 (m-30) cc_final: 0.8254 (t0) REVERT: A 152 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8261 (mtt-85) REVERT: A 179 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7524 (pp) REVERT: A 328 GLU cc_start: 0.8195 (tp30) cc_final: 0.7616 (mt-10) REVERT: A 330 ARG cc_start: 0.4326 (mpt180) cc_final: 0.3058 (ttp-170) REVERT: A 448 MET cc_start: 0.8669 (mmm) cc_final: 0.8284 (mmp) REVERT: B 16 LYS cc_start: 0.8300 (tttm) cc_final: 0.7810 (mmmt) REVERT: B 33 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7289 (mt) REVERT: B 76 ASP cc_start: 0.8519 (m-30) cc_final: 0.8219 (t0) REVERT: B 152 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8250 (mtt-85) REVERT: B 179 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7509 (pp) REVERT: B 328 GLU cc_start: 0.8210 (tp30) cc_final: 0.7621 (mt-10) REVERT: B 330 ARG cc_start: 0.4385 (mpt180) cc_final: 0.3129 (ttp-170) REVERT: B 448 MET cc_start: 0.8674 (mmm) cc_final: 0.8293 (mmp) outliers start: 35 outliers final: 22 residues processed: 136 average time/residue: 0.2152 time to fit residues: 40.5472 Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 109 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 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 33 LEU 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 279 VAL Chi-restraints excluded: chain B residue 285 SER 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: 0.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.170887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139482 restraints weight = 9735.602| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.45 r_work: 0.3397 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3207 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= 0.122 Angle : 0.576 6.570 10018 Z= 0.301 Chirality : 0.041 0.254 1204 Planarity : 0.005 0.083 1232 Dihedral : 4.604 30.301 1030 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 4.31 % Allowed : 22.19 % 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: -0.14 (0.28), residues: 966 helix: 1.36 (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 0.003 0.001 TRP B 253 HIS 0.002 0.001 HIS A 17 PHE 0.008 0.001 PHE A 51 TYR 0.014 0.001 TYR B 375 ARG 0.009 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 380) hydrogen bonds : angle 3.87307 ( 1122) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.64283 ( 12) covalent geometry : bond 0.00284 ( 7366) covalent geometry : angle 0.57337 (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 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.730 Fit side-chains REVERT: A 16 LYS cc_start: 0.8295 (tttm) cc_final: 0.7799 (mmmt) REVERT: A 33 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7242 (mt) REVERT: A 76 ASP cc_start: 0.8519 (m-30) cc_final: 0.8237 (t0) REVERT: A 152 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8298 (mtt-85) REVERT: A 179 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7510 (pp) REVERT: A 328 GLU cc_start: 0.8209 (tp30) cc_final: 0.7706 (mt-10) REVERT: A 330 ARG cc_start: 0.4419 (mpt180) cc_final: 0.3117 (ttp-170) REVERT: A 448 MET cc_start: 0.8602 (mmm) cc_final: 0.8203 (mmp) REVERT: B 16 LYS cc_start: 0.8302 (tttm) cc_final: 0.7810 (mmmt) REVERT: B 33 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7259 (mt) REVERT: B 76 ASP cc_start: 0.8535 (m-30) cc_final: 0.8178 (t0) REVERT: B 152 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8311 (mtt-85) REVERT: B 179 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7568 (pp) REVERT: B 328 GLU cc_start: 0.8232 (tp30) cc_final: 0.7725 (mt-10) REVERT: B 330 ARG cc_start: 0.4403 (mpt180) cc_final: 0.3134 (ttp-170) REVERT: B 448 MET cc_start: 0.8599 (mmm) cc_final: 0.8206 (mmp) outliers start: 33 outliers final: 20 residues processed: 136 average time/residue: 0.2134 time to fit residues: 40.3201 Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 219 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.168895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140205 restraints weight = 9399.902| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.23 r_work: 0.3424 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3325 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= 0.120 Angle : 0.593 8.793 10018 Z= 0.311 Chirality : 0.041 0.243 1204 Planarity : 0.005 0.084 1232 Dihedral : 4.589 30.379 1030 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.79 % Allowed : 23.11 % Favored : 73.11 % 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 (0.27), residues: 966 helix: 1.35 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -2.54 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 253 HIS 0.003 0.001 HIS A 17 PHE 0.008 0.001 PHE A 51 TYR 0.014 0.001 TYR B 375 ARG 0.008 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 380) hydrogen bonds : angle 3.87680 ( 1122) SS BOND : bond 0.00275 ( 6) SS BOND : angle 1.64725 ( 12) covalent geometry : bond 0.00276 ( 7366) covalent geometry : angle 0.59074 (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 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.879 Fit side-chains REVERT: A 16 LYS cc_start: 0.8286 (tttm) cc_final: 0.7803 (mmmt) REVERT: A 33 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7261 (mt) REVERT: A 76 ASP cc_start: 0.8463 (m-30) cc_final: 0.8227 (t0) REVERT: A 152 ARG cc_start: 0.8710 (mtt180) cc_final: 0.8293 (mtt-85) REVERT: A 179 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7518 (pp) REVERT: A 328 GLU cc_start: 0.8169 (tp30) cc_final: 0.7686 (mt-10) REVERT: A 330 ARG cc_start: 0.4379 (mpt180) cc_final: 0.3138 (ttp-170) REVERT: A 369 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7330 (mm-30) REVERT: A 448 MET cc_start: 0.8582 (mmm) cc_final: 0.8189 (mmp) REVERT: B 16 LYS cc_start: 0.8296 (tttm) cc_final: 0.7816 (mmmt) REVERT: B 33 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7264 (mt) REVERT: B 76 ASP cc_start: 0.8497 (m-30) cc_final: 0.8189 (t0) REVERT: B 152 ARG cc_start: 0.8699 (mtt180) cc_final: 0.8286 (mtt-85) REVERT: B 179 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7566 (pp) REVERT: B 328 GLU cc_start: 0.8203 (tp30) cc_final: 0.7713 (mt-10) REVERT: B 330 ARG cc_start: 0.4369 (mpt180) cc_final: 0.3168 (ttp-170) REVERT: B 369 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7334 (mm-30) REVERT: B 448 MET cc_start: 0.8601 (mmm) cc_final: 0.8211 (mmp) outliers start: 29 outliers final: 23 residues processed: 130 average time/residue: 0.2144 time to fit residues: 38.5372 Evaluate side-chains 128 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 267 MET 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 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 219 VAL Chi-restraints excluded: chain B residue 267 MET 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 76 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.171595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139814 restraints weight = 9733.278| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.46 r_work: 0.3403 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3377 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= 0.122 Angle : 0.603 8.895 10018 Z= 0.315 Chirality : 0.041 0.237 1204 Planarity : 0.005 0.086 1232 Dihedral : 4.594 30.425 1030 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.92 % Allowed : 22.85 % 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: -0.13 (0.27), residues: 966 helix: 1.36 (0.22), residues: 586 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 458 HIS 0.003 0.001 HIS A 17 PHE 0.008 0.001 PHE A 51 TYR 0.014 0.001 TYR A 375 ARG 0.009 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 380) hydrogen bonds : angle 3.87610 ( 1122) SS BOND : bond 0.00207 ( 6) SS BOND : angle 1.48774 ( 12) covalent geometry : bond 0.00282 ( 7366) covalent geometry : angle 0.60086 (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 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8283 (tttm) cc_final: 0.7812 (mmmt) REVERT: A 33 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7254 (mt) REVERT: A 76 ASP cc_start: 0.8474 (m-30) cc_final: 0.8222 (t0) REVERT: A 152 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8312 (mtt-85) REVERT: A 179 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7550 (pp) REVERT: A 218 LEU cc_start: 0.9190 (tp) cc_final: 0.8880 (tp) REVERT: A 328 GLU cc_start: 0.8191 (tp30) cc_final: 0.7651 (mt-10) REVERT: A 330 ARG cc_start: 0.4384 (mpt180) cc_final: 0.3138 (ttp-170) REVERT: A 448 MET cc_start: 0.8565 (mmm) cc_final: 0.8180 (mmp) REVERT: B 16 LYS cc_start: 0.8293 (tttm) cc_final: 0.7826 (mmmt) REVERT: B 33 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7252 (mt) REVERT: B 76 ASP cc_start: 0.8519 (m-30) cc_final: 0.8190 (t0) REVERT: B 152 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8291 (mtt-85) REVERT: B 179 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7556 (pp) REVERT: B 328 GLU cc_start: 0.8232 (tp30) cc_final: 0.7751 (mt-10) REVERT: B 330 ARG cc_start: 0.4400 (mpt180) cc_final: 0.3240 (ttp-170) REVERT: B 448 MET cc_start: 0.8576 (mmm) cc_final: 0.8190 (mmp) outliers start: 30 outliers final: 24 residues processed: 131 average time/residue: 0.2043 time to fit residues: 37.3125 Evaluate side-chains 128 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 109 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 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 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 274 MET 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: 0.0980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 0.0060 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146575 restraints weight = 9505.851| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.48 r_work: 0.3489 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7372 Z= 0.099 Angle : 0.561 9.256 10018 Z= 0.289 Chirality : 0.040 0.220 1204 Planarity : 0.004 0.060 1232 Dihedral : 4.272 30.289 1030 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.13 % Allowed : 23.63 % 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: 0.06 (0.28), residues: 966 helix: 1.59 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 458 HIS 0.003 0.001 HIS A 17 PHE 0.005 0.001 PHE B 31 TYR 0.010 0.001 TYR B 343 ARG 0.008 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.02560 ( 380) hydrogen bonds : angle 3.86332 ( 1122) SS BOND : bond 0.00186 ( 6) SS BOND : angle 1.28120 ( 12) covalent geometry : bond 0.00214 ( 7366) covalent geometry : angle 0.56007 (10006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.30 seconds wall clock time: 69 minutes 1.30 seconds (4141.30 seconds total)