Starting phenix.real_space_refine on Thu Jul 2 11:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p15_13156/07_2026/7p15_13156.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 14 5.16 5 C 5451 2.51 5 N 1439 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8587 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 515} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3398 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 699 Classifications: {'DNA': 32, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'4OI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.18 Number of scatterers: 8587 At special positions: 0 Unit cell: (95.06, 104.76, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 34 15.00 O 1649 8.00 N 1439 7.00 C 5451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 393.2 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.7% alpha, 13.1% beta 12 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.525A pdb=" N ARG A 125 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.712A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.861A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.792A pdb=" N SER A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 4.222A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 505 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.983A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.831A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.312A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.054A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 216 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.532A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.641A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.802A pdb=" N LEU A 74 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.725A pdb=" N GLN A 330 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 354 " --> pdb=" O TRP A 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 4.507A pdb=" N GLU A 344 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.842A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.589A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 457 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 447 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 63 Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.645A pdb=" N LEU B 187 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR B 232 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.968A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 350 removed outlier: 7.450A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 350 removed outlier: 7.450A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 330 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 328 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1379 1.32 - 1.44: 2448 1.44 - 1.56: 4961 1.56 - 1.69: 68 1.69 - 1.81: 26 Bond restraints: 8882 Sorted by residual: bond pdb=" O3' DC F 15 " pdb=" P DT F 16 " ideal model delta sigma weight residual 1.607 1.480 0.127 1.50e-02 4.44e+03 7.19e+01 bond pdb=" C4' DG F 12 " pdb=" O4' DG F 12 " ideal model delta sigma weight residual 1.446 1.381 0.065 1.00e-02 1.00e+04 4.20e+01 bond pdb=" C4' DG F 24 " pdb=" O4' DG F 24 " ideal model delta sigma weight residual 1.446 1.382 0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" C4' DC F 23 " pdb=" O4' DC F 23 " ideal model delta sigma weight residual 1.446 1.386 0.060 1.00e-02 1.00e+04 3.62e+01 bond pdb=" C03 4OI F 101 " pdb=" C05 4OI F 101 " ideal model delta sigma weight residual 1.492 1.610 -0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 8877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 12083 3.56 - 7.12: 112 7.12 - 10.68: 15 10.68 - 14.24: 3 14.24 - 17.80: 2 Bond angle restraints: 12215 Sorted by residual: angle pdb=" O4' DG F 31 " pdb=" C4' DG F 31 " pdb=" C3' DG F 31 " ideal model delta sigma weight residual 106.00 99.86 6.14 6.00e-01 2.78e+00 1.05e+02 angle pdb=" C5' DA F 21 " pdb=" C4' DA F 21 " pdb=" O4' DA F 21 " ideal model delta sigma weight residual 109.30 127.10 -17.80 1.90e+00 2.77e-01 8.77e+01 angle pdb=" C3' DC F 15 " pdb=" O3' DC F 15 " pdb=" P DT F 16 " ideal model delta sigma weight residual 120.20 132.96 -12.76 1.50e+00 4.44e-01 7.24e+01 angle pdb=" O4' DC F 5 " pdb=" C4' DC F 5 " pdb=" C3' DC F 5 " ideal model delta sigma weight residual 106.00 101.61 4.39 6.00e-01 2.78e+00 5.35e+01 angle pdb=" N ASP B 186 " pdb=" CA ASP B 186 " pdb=" C ASP B 186 " ideal model delta sigma weight residual 109.24 120.86 -11.62 1.63e+00 3.76e-01 5.08e+01 ... (remaining 12210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4532 17.94 - 35.89: 527 35.89 - 53.83: 130 53.83 - 71.78: 30 71.78 - 89.72: 9 Dihedral angle restraints: 5228 sinusoidal: 2397 harmonic: 2831 Sorted by residual: dihedral pdb=" C TYR A 181 " pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" CB TYR A 181 " ideal model delta harmonic sigma weight residual -122.60 -109.61 -12.99 0 2.50e+00 1.60e-01 2.70e+01 dihedral pdb=" C GLU B 169 " pdb=" N GLU B 169 " pdb=" CA GLU B 169 " pdb=" CB GLU B 169 " ideal model delta harmonic sigma weight residual -122.60 -132.60 10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CA GLU B 344 " pdb=" C GLU B 344 " pdb=" N PRO B 345 " pdb=" CA PRO B 345 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1303 0.158 - 0.317: 24 0.317 - 0.475: 9 0.475 - 0.633: 2 0.633 - 0.791: 1 Chirality restraints: 1339 Sorted by residual: chirality pdb=" C4' DA F 21 " pdb=" C5' DA F 21 " pdb=" O4' DA F 21 " pdb=" C3' DA F 21 " both_signs ideal model delta sigma weight residual False -2.53 -1.74 -0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C4' DC F 20 " pdb=" C5' DC F 20 " pdb=" O4' DC F 20 " pdb=" C3' DC F 20 " both_signs ideal model delta sigma weight residual False -2.53 -1.96 -0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" C4' DC F 22 " pdb=" C5' DC F 22 " pdb=" O4' DC F 22 " pdb=" C3' DC F 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.01 -0.52 2.00e-01 2.50e+01 6.79e+00 ... (remaining 1336 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 78 " 0.540 9.50e-02 1.11e+02 2.42e-01 3.58e+01 pdb=" NE ARG A 78 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 78 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 78 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 78 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 536 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 537 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 475 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLN A 475 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN A 475 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 476 " -0.019 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 842 2.74 - 3.28: 8071 3.28 - 3.82: 14246 3.82 - 4.36: 16601 4.36 - 4.90: 28282 Nonbonded interactions: 68042 Sorted by model distance: nonbonded pdb=" O LEU B 80 " pdb=" OG1 THR B 84 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP B 17 " pdb=" OH TYR B 56 " model vdw 2.245 3.040 nonbonded pdb=" O LEU A 486 " pdb=" NZ LYS A 528 " model vdw 2.247 3.120 nonbonded pdb=" O LYS A 540 " pdb=" OG SER B 280 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 253 " pdb=" OD1 ASP B 256 " model vdw 2.290 3.040 ... (remaining 68037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.006 0.127 8882 Z= 0.376 Angle : 0.941 17.798 12215 Z= 0.584 Chirality : 0.072 0.791 1339 Planarity : 0.009 0.242 1420 Dihedral : 16.286 89.724 3402 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.23 % Allowed : 1.75 % Favored : 98.01 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.26), residues: 963 helix: 0.33 (0.27), residues: 352 sheet: -1.34 (0.45), residues: 132 loop : -1.40 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 125 TYR 0.027 0.002 TYR B 339 PHE 0.021 0.002 PHE A 77 TRP 0.047 0.002 TRP B 414 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.38 ( 8882) covalent geometry : angle 0.94055 / 0.58 (12215) hydrogen bonds : bond 0.17860 / 12.59 ( 331) hydrogen bonds : angle 7.26020 / 5.04 ( 880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 THR cc_start: 0.7879 (m) cc_final: 0.7417 (m) REVERT: A 232 TYR cc_start: 0.8293 (m-10) cc_final: 0.7963 (m-10) REVERT: A 537 PRO cc_start: 0.8730 (Cg_exo) cc_final: 0.8498 (Cg_endo) REVERT: B 22 LYS cc_start: 0.7901 (tttm) cc_final: 0.7600 (pttt) REVERT: B 185 ASP cc_start: 0.6693 (m-30) cc_final: 0.6230 (m-30) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.0989 time to fit residues: 17.1200 Evaluate side-chains 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 161 GLN A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.208024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171247 restraints weight = 10168.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173587 restraints weight = 9307.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.175616 restraints weight = 6883.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175371 restraints weight = 5793.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.175695 restraints weight = 5159.807| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8882 Z= 0.140 Angle : 0.603 8.216 12215 Z= 0.330 Chirality : 0.046 0.172 1339 Planarity : 0.005 0.055 1420 Dihedral : 14.058 59.786 1388 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.82 % Allowed : 7.13 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 963 helix: 0.90 (0.28), residues: 352 sheet: -0.91 (0.45), residues: 144 loop : -1.27 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.026 0.002 TYR A 319 PHE 0.010 0.002 PHE A 124 TRP 0.019 0.001 TRP B 414 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8882) covalent geometry : angle 0.60315 / 0.33 (12215) hydrogen bonds : bond 0.04484 / 2.98 ( 331) hydrogen bonds : angle 5.00035 / 3.44 ( 880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.317 Fit side-chains REVERT: A 10 VAL cc_start: 0.8291 (p) cc_final: 0.7907 (m) REVERT: B 22 LYS cc_start: 0.7908 (tttm) cc_final: 0.7581 (pttt) REVERT: B 357 MET cc_start: 0.6243 (tpp) cc_final: 0.6030 (tpp) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 0.0861 time to fit residues: 13.6294 Evaluate side-chains 98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN B 161 GLN B 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.203907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165579 restraints weight = 10121.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166577 restraints weight = 8599.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.168982 restraints weight = 6795.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169612 restraints weight = 5121.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170038 restraints weight = 4794.530| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8882 Z= 0.183 Angle : 0.623 7.743 12215 Z= 0.336 Chirality : 0.045 0.162 1339 Planarity : 0.005 0.047 1420 Dihedral : 14.140 59.801 1386 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.29 % Allowed : 9.12 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 963 helix: 0.84 (0.28), residues: 352 sheet: -1.16 (0.44), residues: 144 loop : -1.27 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.022 0.002 TYR B 339 PHE 0.018 0.002 PHE A 160 TRP 0.022 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 8882) covalent geometry : angle 0.62323 / 0.34 (12215) hydrogen bonds : bond 0.04603 / 3.02 ( 331) hydrogen bonds : angle 4.83234 / 3.35 ( 880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.314 Fit side-chains REVERT: B 22 LYS cc_start: 0.7938 (tttm) cc_final: 0.7514 (pttt) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.0687 time to fit residues: 11.0410 Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164959 restraints weight = 10357.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165902 restraints weight = 9315.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168289 restraints weight = 7131.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169409 restraints weight = 5068.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169636 restraints weight = 4790.519| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8882 Z= 0.174 Angle : 0.602 6.846 12215 Z= 0.326 Chirality : 0.045 0.163 1339 Planarity : 0.005 0.042 1420 Dihedral : 14.230 59.102 1386 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 11.81 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 963 helix: 0.85 (0.28), residues: 352 sheet: -1.33 (0.44), residues: 144 loop : -1.19 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.020 0.002 TYR A 319 PHE 0.017 0.002 PHE A 160 TRP 0.021 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8882) covalent geometry : angle 0.60221 / 0.33 (12215) hydrogen bonds : bond 0.04277 / 2.79 ( 331) hydrogen bonds : angle 4.69813 / 3.28 ( 880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.307 Fit side-chains REVERT: A 340 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 22 LYS cc_start: 0.7934 (tttm) cc_final: 0.7516 (pttt) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.0734 time to fit residues: 11.6350 Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.206462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168061 restraints weight = 10089.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169191 restraints weight = 8460.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171701 restraints weight = 6538.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172540 restraints weight = 4816.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172874 restraints weight = 4640.406| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8882 Z= 0.125 Angle : 0.549 6.407 12215 Z= 0.299 Chirality : 0.043 0.168 1339 Planarity : 0.004 0.040 1420 Dihedral : 14.133 59.382 1386 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.40 % Allowed : 13.80 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 963 helix: 1.18 (0.28), residues: 348 sheet: -1.08 (0.43), residues: 149 loop : -0.97 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.014 0.001 TYR B 342 PHE 0.010 0.001 PHE B 124 TRP 0.018 0.001 TRP A 402 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8882) covalent geometry : angle 0.54885 / 0.30 (12215) hydrogen bonds : bond 0.03715 / 2.43 ( 331) hydrogen bonds : angle 4.50327 / 3.12 ( 880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.8117 (t60) cc_final: 0.7441 (t60) REVERT: A 340 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: B 22 LYS cc_start: 0.7921 (tttm) cc_final: 0.7499 (pttt) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.0736 time to fit residues: 12.3882 Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 17 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 242 GLN A 258 GLN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.208612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171678 restraints weight = 10050.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173440 restraints weight = 9101.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.175676 restraints weight = 7119.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.175713 restraints weight = 5652.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176036 restraints weight = 5218.149| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8882 Z= 0.109 Angle : 0.527 6.342 12215 Z= 0.287 Chirality : 0.043 0.167 1339 Planarity : 0.004 0.040 1420 Dihedral : 14.068 59.046 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.52 % Allowed : 14.62 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.27), residues: 963 helix: 1.37 (0.28), residues: 348 sheet: -0.78 (0.45), residues: 138 loop : -0.89 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.015 0.001 TYR B 342 PHE 0.009 0.001 PHE B 124 TRP 0.017 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 8882) covalent geometry : angle 0.52670 / 0.29 (12215) hydrogen bonds : bond 0.03373 / 2.23 ( 331) hydrogen bonds : angle 4.39748 / 3.05 ( 880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6566 (pp) REVERT: A 340 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: B 22 LYS cc_start: 0.7897 (tttm) cc_final: 0.7468 (pttt) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.0753 time to fit residues: 13.5417 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 21 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.204627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.166164 restraints weight = 10291.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167297 restraints weight = 8666.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169663 restraints weight = 6865.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170075 restraints weight = 5192.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170384 restraints weight = 4778.320| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8882 Z= 0.170 Angle : 0.601 7.035 12215 Z= 0.323 Chirality : 0.045 0.164 1339 Planarity : 0.005 0.047 1420 Dihedral : 14.178 59.330 1386 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.75 % Allowed : 15.32 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 963 helix: 1.29 (0.28), residues: 342 sheet: -1.15 (0.41), residues: 154 loop : -0.85 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 125 TYR 0.024 0.002 TYR A 232 PHE 0.016 0.002 PHE A 160 TRP 0.021 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8882) covalent geometry : angle 0.60083 / 0.32 (12215) hydrogen bonds : bond 0.04011 / 2.61 ( 331) hydrogen bonds : angle 4.50772 / 3.11 ( 880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7216 (pt) REVERT: A 229 TRP cc_start: 0.8162 (t60) cc_final: 0.7461 (t60) REVERT: A 339 TYR cc_start: 0.7387 (m-10) cc_final: 0.6857 (m-10) REVERT: A 340 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: B 22 LYS cc_start: 0.7890 (tttm) cc_final: 0.7524 (pttt) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.0935 time to fit residues: 14.9386 Evaluate side-chains 108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN A 306 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.202067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162281 restraints weight = 10171.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.164545 restraints weight = 8423.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166596 restraints weight = 6169.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166622 restraints weight = 4815.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166958 restraints weight = 4963.604| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8882 Z= 0.210 Angle : 0.652 8.806 12215 Z= 0.349 Chirality : 0.046 0.166 1339 Planarity : 0.005 0.050 1420 Dihedral : 14.391 60.727 1386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.87 % Allowed : 15.56 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 963 helix: 0.98 (0.28), residues: 339 sheet: -1.33 (0.41), residues: 152 loop : -0.99 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 125 TYR 0.032 0.002 TYR A 232 PHE 0.023 0.002 PHE A 160 TRP 0.022 0.002 TRP A 402 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 8882) covalent geometry : angle 0.65159 / 0.35 (12215) hydrogen bonds : bond 0.04544 / 2.97 ( 331) hydrogen bonds : angle 4.69415 / 3.26 ( 880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7092 (pt) REVERT: A 229 TRP cc_start: 0.8216 (t60) cc_final: 0.7567 (t60) REVERT: A 340 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: B 22 LYS cc_start: 0.7926 (tttm) cc_final: 0.7564 (pttt) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.0786 time to fit residues: 12.1918 Evaluate side-chains 106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.204142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.166425 restraints weight = 10182.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167455 restraints weight = 8677.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.168765 restraints weight = 7937.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169624 restraints weight = 6161.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170330 restraints weight = 5200.135| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8882 Z= 0.155 Angle : 0.597 8.287 12215 Z= 0.321 Chirality : 0.044 0.167 1339 Planarity : 0.005 0.047 1420 Dihedral : 14.342 60.797 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 16.49 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 963 helix: 1.11 (0.29), residues: 340 sheet: -1.35 (0.41), residues: 154 loop : -0.94 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 125 TYR 0.026 0.002 TYR A 232 PHE 0.014 0.002 PHE A 160 TRP 0.028 0.001 TRP B 212 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8882) covalent geometry : angle 0.59655 / 0.32 (12215) hydrogen bonds : bond 0.04017 / 2.63 ( 331) hydrogen bonds : angle 4.55387 / 3.16 ( 880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.8125 (t60) cc_final: 0.7518 (t60) REVERT: A 340 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: B 22 LYS cc_start: 0.7898 (tttm) cc_final: 0.7507 (pttt) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.0831 time to fit residues: 12.8263 Evaluate side-chains 104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 29 optimal weight: 7.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.206355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168144 restraints weight = 10055.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169940 restraints weight = 8648.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172177 restraints weight = 6505.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172457 restraints weight = 4846.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172701 restraints weight = 4568.403| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8882 Z= 0.125 Angle : 0.566 8.772 12215 Z= 0.304 Chirality : 0.043 0.172 1339 Planarity : 0.005 0.079 1420 Dihedral : 14.271 60.497 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.17 % Allowed : 16.96 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.27), residues: 963 helix: 1.33 (0.29), residues: 341 sheet: -1.06 (0.43), residues: 143 loop : -0.86 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 211 TYR 0.020 0.001 TYR A 232 PHE 0.015 0.001 PHE A 130 TRP 0.032 0.001 TRP B 212 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8882) covalent geometry : angle 0.56579 / 0.30 (12215) hydrogen bonds : bond 0.03540 / 2.33 ( 331) hydrogen bonds : angle 4.42814 / 3.07 ( 880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.8099 (t60) cc_final: 0.7541 (t60) REVERT: A 340 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: B 22 LYS cc_start: 0.7861 (tttm) cc_final: 0.7478 (pttt) REVERT: B 356 ARG cc_start: 0.5854 (ptm160) cc_final: 0.5552 (ttm170) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.0894 time to fit residues: 14.5658 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.205618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168198 restraints weight = 10073.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168389 restraints weight = 8717.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170729 restraints weight = 7133.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171094 restraints weight = 5634.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171766 restraints weight = 5006.143| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8882 Z= 0.139 Angle : 0.590 8.745 12215 Z= 0.316 Chirality : 0.044 0.170 1339 Planarity : 0.005 0.067 1420 Dihedral : 14.307 60.376 1386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.40 % Allowed : 17.19 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 963 helix: 1.33 (0.29), residues: 341 sheet: -1.07 (0.42), residues: 143 loop : -0.87 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 125 TYR 0.021 0.002 TYR A 232 PHE 0.016 0.001 PHE A 130 TRP 0.031 0.001 TRP B 212 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8882) covalent geometry : angle 0.59016 / 0.32 (12215) hydrogen bonds : bond 0.03701 / 2.40 ( 331) hydrogen bonds : angle 4.48369 / 3.08 ( 880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.87 seconds wall clock time: 21 minutes 9.02 seconds (1269.02 seconds total)