Starting phenix.real_space_refine on Fri Sep 11 07:41:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p15_13156/09_2026/7p15_13156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p15_13156/09_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_13156/09_2026/7p15_13156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p15_13156/09_2026/7p15_13156.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p15_13156/09_2026/7p15_13156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p15_13156/09_2026/7p15_13156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p15_13156/09_2026/7p15_13156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p15_13156/09_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-2.2.1-6174/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: 2.00, per 1000 atoms: 0.23 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: 0.87 Conformation dependent library (CDL) restraints added in 266.7 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: 0.88 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: 1.35 Time building geometry restraints manager: 1.12 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 1.20e-02 6.94e+03 1.12e+02 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=" O3' DG F 31 " pdb=" P DG F 32 " ideal model delta sigma weight residual 1.607 1.681 -0.074 1.20e-02 6.94e+03 3.78e+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 ... (remaining 8877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 12082 3.56 - 7.12: 113 7.12 - 10.68: 15 10.68 - 14.24: 3 14.24 - 17.80: 2 Bond angle restraints: 12215 Sorted by residual: angle pdb=" C3' DC F 15 " pdb=" O3' DC F 15 " pdb=" P DT F 16 " ideal model delta sigma weight residual 119.70 132.96 -13.26 1.20e+00 6.94e-01 1.22e+02 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=" 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: 0.120 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- 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= 0.389 Angle : 0.943 17.798 12215 Z= 0.590 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 / 0.39 ( 8882) covalent geometry : angle 0.94312 / 0.59 (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 : 0.317 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: 0.7964 (m-10) REVERT: A 284 ARG cc_start: 0.6441 (tpp-160) cc_final: 0.4687 (mmt90) 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: 0.7601 (pttt) REVERT: B 185 ASP cc_start: 0.6693 (m-30) cc_final: 0.6231 (m-30) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.1044 time to fit residues: 18.2151 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 : 0.338 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.207581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170830 restraints weight = 10171.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173413 restraints weight = 9426.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175398 restraints weight = 7015.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.175159 restraints weight = 5586.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175493 restraints weight = 5288.872| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8882 Z= 0.136 Angle : 0.608 7.937 12215 Z= 0.331 Chirality : 0.046 0.188 1339 Planarity : 0.005 0.056 1420 Dihedral : 14.049 59.945 1388 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -0.64 (0.27), residues: 963 helix: 0.89 (0.28), residues: 352 sheet: -0.90 (0.45), residues: 144 loop : -1.30 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 307 TYR 0.027 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 0.00293 / 0.14 ( 8882) covalent geometry : angle 0.60778 / 0.33 (12215) hydrogen bonds : bond 0.04566 / 3.02 ( 331) hydrogen bonds : angle 5.00647 / 3.45 ( 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 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.260 Fit side-chains REVERT: A 10 VAL cc_start: 0.8292 (p) cc_final: 0.7906 (m) REVERT: A 284 ARG cc_start: 0.6606 (tpp-160) cc_final: 0.5036 (mmt90) REVERT: B 22 LYS cc_start: 0.7903 (tttm) cc_final: 0.7570 (pttt) REVERT: B 357 MET cc_start: 0.6240 (tpp) cc_final: 0.6024 (tpp) outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.0905 time to fit residues: 14.1987 Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 8.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 0.0470 chunk 73 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.205701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167568 restraints weight = 10090.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168524 restraints weight = 8548.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171331 restraints weight = 6789.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171402 restraints weight = 4952.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171830 restraints weight = 4773.756| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8882 Z= 0.152 Angle : 0.589 7.091 12215 Z= 0.318 Chirality : 0.044 0.159 1339 Planarity : 0.005 0.046 1420 Dihedral : 14.033 59.997 1386 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.17 % Allowed : 8.89 % Favored : 89.94 % 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: -0.57 (0.27), residues: 963 helix: 1.01 (0.28), residues: 352 sheet: -1.00 (0.44), residues: 143 loop : -1.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 83 TYR 0.019 0.002 TYR A 232 PHE 0.013 0.002 PHE A 160 TRP 0.020 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8882) covalent geometry : angle 0.58865 / 0.32 (12215) hydrogen bonds : bond 0.04273 / 2.82 ( 331) hydrogen bonds : angle 4.74772 / 3.29 ( 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 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.348 Fit side-chains REVERT: A 339 TYR cc_start: 0.7491 (m-10) cc_final: 0.7171 (m-10) REVERT: B 22 LYS cc_start: 0.7942 (tttm) cc_final: 0.7527 (pttt) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.0849 time to fit residues: 13.2747 Evaluate side-chains 102 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 2.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.206215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167867 restraints weight = 10302.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169922 restraints weight = 8605.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172512 restraints weight = 6392.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172343 restraints weight = 4745.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172824 restraints weight = 4904.119| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8882 Z= 0.139 Angle : 0.567 6.543 12215 Z= 0.308 Chirality : 0.044 0.178 1339 Planarity : 0.004 0.040 1420 Dihedral : 14.071 59.772 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 11.58 % Favored : 86.90 % 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: -0.46 (0.27), residues: 963 helix: 1.07 (0.28), residues: 354 sheet: -1.09 (0.44), residues: 143 loop : -1.10 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.023 0.001 TYR A 232 PHE 0.012 0.001 PHE A 160 TRP 0.019 0.001 TRP A 402 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8882) covalent geometry : angle 0.56741 / 0.31 (12215) hydrogen bonds : bond 0.03924 / 2.55 ( 331) hydrogen bonds : angle 4.57566 / 3.18 ( 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 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.323 Fit side-chains REVERT: A 339 TYR cc_start: 0.7411 (m-10) cc_final: 0.6936 (m-10) REVERT: A 340 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 22 LYS cc_start: 0.7932 (tttm) cc_final: 0.7516 (pttt) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.0811 time to fit residues: 13.5509 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.203117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.164422 restraints weight = 10185.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.166188 restraints weight = 8753.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168653 restraints weight = 6610.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168790 restraints weight = 4937.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169244 restraints weight = 4955.974| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8882 Z= 0.190 Angle : 0.620 7.119 12215 Z= 0.334 Chirality : 0.045 0.155 1339 Planarity : 0.005 0.043 1420 Dihedral : 14.216 59.254 1386 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.87 % Allowed : 13.22 % Favored : 84.91 % 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: -0.57 (0.27), residues: 963 helix: 0.99 (0.28), residues: 346 sheet: -1.28 (0.43), residues: 149 loop : -1.08 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.021 0.002 TYR B 339 PHE 0.019 0.002 PHE A 160 TRP 0.022 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 8882) covalent geometry : angle 0.61994 / 0.33 (12215) hydrogen bonds : bond 0.04384 / 2.85 ( 331) hydrogen bonds : angle 4.65297 / 3.23 ( 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 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.239 Fit side-chains REVERT: A 340 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 356 ARG cc_start: 0.7293 (tpt-90) cc_final: 0.7085 (tpt-90) REVERT: B 22 LYS cc_start: 0.7944 (tttm) cc_final: 0.7522 (pttt) outliers start: 16 outliers final: 14 residues processed: 114 average time/residue: 0.0791 time to fit residues: 13.2952 Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 156 SER 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 Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 ILE 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: 4.9990 chunk 2 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 63 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.203535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.164840 restraints weight = 10135.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.166750 restraints weight = 8624.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169247 restraints weight = 6446.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169277 restraints weight = 4815.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169733 restraints weight = 4691.285| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1653 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= 0.157 Angle : 0.585 6.825 12215 Z= 0.318 Chirality : 0.044 0.168 1339 Planarity : 0.005 0.044 1420 Dihedral : 14.212 59.268 1386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.75 % Allowed : 14.62 % Favored : 83.63 % 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: -0.49 (0.27), residues: 963 helix: 1.09 (0.28), residues: 346 sheet: -1.33 (0.42), residues: 149 loop : -1.03 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.016 0.002 TYR B 339 PHE 0.014 0.001 PHE A 160 TRP 0.020 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8882) covalent geometry : angle 0.58542 / 0.32 (12215) hydrogen bonds : bond 0.04087 / 2.68 ( 331) hydrogen bonds : angle 4.57704 / 3.18 ( 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 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 340 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: B 22 LYS cc_start: 0.7916 (tttm) cc_final: 0.7504 (pttt) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.0826 time to fit residues: 13.6021 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 156 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 258 GLN ** A 306 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.201788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162748 restraints weight = 10294.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164467 restraints weight = 9105.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165832 restraints weight = 7227.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167272 restraints weight = 5307.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.167434 restraints weight = 4853.615| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8882 Z= 0.195 Angle : 0.638 7.503 12215 Z= 0.342 Chirality : 0.046 0.168 1339 Planarity : 0.005 0.047 1420 Dihedral : 14.347 59.947 1386 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.46 % Allowed : 14.97 % 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: -0.67 (0.27), residues: 963 helix: 0.92 (0.28), residues: 346 sheet: -1.47 (0.42), residues: 149 loop : -1.09 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.022 0.002 TYR B 339 PHE 0.020 0.002 PHE A 160 TRP 0.022 0.001 TRP A 402 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 8882) covalent geometry : angle 0.63757 / 0.34 (12215) hydrogen bonds : bond 0.04427 / 2.89 ( 331) hydrogen bonds : angle 4.65078 / 3.24 ( 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 116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7239 (pt) REVERT: A 229 TRP cc_start: 0.8196 (t60) cc_final: 0.7540 (t60) REVERT: A 340 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: A 356 ARG cc_start: 0.7321 (tpt-90) cc_final: 0.7116 (tpt-90) REVERT: B 22 LYS cc_start: 0.7917 (tttm) cc_final: 0.7483 (pttt) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 0.0779 time to fit residues: 13.0848 Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 258 GLN A 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.201975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.163190 restraints weight = 10129.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.165047 restraints weight = 9041.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167135 restraints weight = 6837.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167234 restraints weight = 5247.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167435 restraints weight = 4876.510| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8882 Z= 0.192 Angle : 0.625 8.247 12215 Z= 0.336 Chirality : 0.046 0.168 1339 Planarity : 0.005 0.049 1420 Dihedral : 14.414 60.242 1386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.34 % Allowed : 15.20 % Favored : 82.46 % 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: -0.59 (0.27), residues: 963 helix: 0.99 (0.28), residues: 339 sheet: -1.38 (0.41), residues: 152 loop : -1.04 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.020 0.002 TYR B 339 PHE 0.019 0.002 PHE A 160 TRP 0.025 0.002 TRP B 212 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 8882) covalent geometry : angle 0.62491 / 0.34 (12215) hydrogen bonds : bond 0.04376 / 2.86 ( 331) hydrogen bonds : angle 4.64686 / 3.24 ( 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 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 229 TRP cc_start: 0.8188 (t60) cc_final: 0.7601 (t60) REVERT: A 340 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 22 LYS cc_start: 0.7924 (tttm) cc_final: 0.7523 (pttt) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.0821 time to fit residues: 13.6582 Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 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 47 ILE 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 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 Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.207228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168784 restraints weight = 10094.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.169914 restraints weight = 8689.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172461 restraints weight = 6775.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172826 restraints weight = 5099.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173236 restraints weight = 4735.997| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8882 Z= 0.115 Angle : 0.553 8.267 12215 Z= 0.298 Chirality : 0.043 0.177 1339 Planarity : 0.004 0.044 1420 Dihedral : 14.243 60.080 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 16.61 % Favored : 82.22 % 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: -0.15 (0.27), residues: 963 helix: 1.35 (0.28), residues: 341 sheet: -1.02 (0.43), residues: 143 loop : -0.85 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.017 0.001 TYR A 232 PHE 0.014 0.001 PHE A 130 TRP 0.030 0.001 TRP B 212 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8882) covalent geometry : angle 0.55262 / 0.30 (12215) hydrogen bonds : bond 0.03489 / 2.32 ( 331) hydrogen bonds : angle 4.43615 / 3.07 ( 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 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 TRP cc_start: 0.8092 (t60) cc_final: 0.7542 (t60) REVERT: A 340 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: B 22 LYS cc_start: 0.7883 (tttm) cc_final: 0.7494 (pttt) outliers start: 10 outliers final: 6 residues processed: 114 average time/residue: 0.0811 time to fit residues: 13.4607 Evaluate side-chains 107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 2 optimal weight: 0.0980 chunk 76 optimal weight: 40.0000 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.208287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170392 restraints weight = 10004.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.171863 restraints weight = 8318.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174020 restraints weight = 6505.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174944 restraints weight = 4756.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175241 restraints weight = 4530.137| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8882 Z= 0.111 Angle : 0.542 9.051 12215 Z= 0.291 Chirality : 0.043 0.165 1339 Planarity : 0.004 0.043 1420 Dihedral : 14.195 59.288 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.94 % Allowed : 17.31 % Favored : 81.75 % 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: 0.04 (0.27), residues: 963 helix: 1.57 (0.28), residues: 341 sheet: -0.88 (0.42), residues: 143 loop : -0.79 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.013 0.001 TYR B 342 PHE 0.014 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 0.00234 / 0.11 ( 8882) covalent geometry : angle 0.54240 / 0.29 (12215) hydrogen bonds : bond 0.03247 / 2.13 ( 331) hydrogen bonds : angle 4.31538 / 2.97 ( 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 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: B 22 LYS cc_start: 0.7890 (tttm) cc_final: 0.7485 (pttt) outliers start: 8 outliers final: 4 residues processed: 120 average time/residue: 0.0895 time to fit residues: 15.3638 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 40.0000 chunk 63 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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 = 0.4382 r_free = 0.4382 target = 0.203930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.164279 restraints weight = 10118.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166556 restraints weight = 8434.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168023 restraints weight = 6474.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.168436 restraints weight = 5096.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.168813 restraints weight = 4912.044| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8882 Z= 0.175 Angle : 0.631 13.021 12215 Z= 0.333 Chirality : 0.045 0.176 1339 Planarity : 0.005 0.049 1420 Dihedral : 14.340 59.632 1386 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.17 % Allowed : 17.54 % Favored : 81.29 % 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: -0.22 (0.27), residues: 963 helix: 1.27 (0.28), residues: 340 sheet: -1.06 (0.43), residues: 143 loop : -0.85 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.027 0.002 TYR A 232 PHE 0.017 0.002 PHE A 160 TRP 0.031 0.001 TRP B 212 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 8882) covalent geometry : angle 0.63070 / 0.33 (12215) hydrogen bonds : bond 0.04014 / 2.62 ( 331) hydrogen bonds : angle 4.53268 / 3.10 ( 880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1277.74 seconds wall clock time: 22 minutes 53.89 seconds (1373.89 seconds total)