Starting phenix.real_space_refine on Thu Jul 24 14:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.map" model { file = "/net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lum_63398/07_2025/9lum_63398.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3858 2.51 5 N 1052 2.21 5 O 1382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6321 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3403 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Time building chain proxies: 6.40, per 1000 atoms: 1.01 Number of scatterers: 6321 At special positions: 0 Unit cell: (63.3335, 87.9218, 104.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1382 8.00 N 1052 7.00 C 3858 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: 1.48 Conformation dependent library (CDL) restraints added in 946.2 milliseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 52.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.681A pdb=" N LEU A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 87 removed outlier: 3.897A pdb=" N GLN A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASP A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.007A pdb=" N ALA A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 277 removed outlier: 4.097A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 300 through 317 Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.114A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.772A pdb=" N GLU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.560A pdb=" N LEU A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.571A pdb=" N LYS A 425 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 428 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.977A pdb=" N LYS A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 481 Processing helix chain 'A' and resid 486 through 506 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.565A pdb=" N PHE A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.705A pdb=" N VAL B 15 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 124 through 139 removed outlier: 3.769A pdb=" N THR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.690A pdb=" N ASN B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 291 through 305 Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.719A pdb=" N HIS B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.595A pdb=" N LEU B 76 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 77 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL B 143 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 109 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 145 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE B 111 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 108 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP B 190 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B 112 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE B 185 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ILE B 215 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 187 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU B 217 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 189 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.615A pdb=" N PHE A 353 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ARG A 390 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 355 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 392 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 357 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.615A pdb=" N PHE A 353 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ARG A 390 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 355 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 392 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 357 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 415 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR A 449 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 417 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 451 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 419 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLN A 453 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 567 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR A 576 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 565 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.916A pdb=" N THR B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 2 1.11 - 1.29: 1023 1.29 - 1.46: 2306 1.46 - 1.63: 2837 1.63 - 1.81: 46 Bond restraints: 6214 Sorted by residual: bond pdb=" CG PRO A 509 " pdb=" CD PRO A 509 " ideal model delta sigma weight residual 1.503 1.059 0.444 3.40e-02 8.65e+02 1.71e+02 bond pdb=" CB PRO A 361 " pdb=" CG PRO A 361 " ideal model delta sigma weight residual 1.492 0.938 0.554 5.00e-02 4.00e+02 1.23e+02 bond pdb=" CG PRO A 361 " pdb=" CD PRO A 361 " ideal model delta sigma weight residual 1.503 1.237 0.266 3.40e-02 8.65e+02 6.11e+01 bond pdb=" CG PRO A 360 " pdb=" CD PRO A 360 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.44e+01 bond pdb=" N PRO A 509 " pdb=" CD PRO A 509 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 ... (remaining 6209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.91: 8435 11.91 - 23.82: 2 23.82 - 35.72: 4 35.72 - 47.63: 1 47.63 - 59.54: 1 Bond angle restraints: 8443 Sorted by residual: angle pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " pdb=" CG PRO A 361 " ideal model delta sigma weight residual 104.50 68.44 36.06 1.90e+00 2.77e-01 3.60e+02 angle pdb=" CB PRO A 361 " pdb=" CG PRO A 361 " pdb=" CD PRO A 361 " ideal model delta sigma weight residual 106.10 165.64 -59.54 3.20e+00 9.77e-02 3.46e+02 angle pdb=" N PRO A 509 " pdb=" CD PRO A 509 " pdb=" CG PRO A 509 " ideal model delta sigma weight residual 103.20 75.33 27.87 1.50e+00 4.44e-01 3.45e+02 angle pdb=" N PRO A 361 " pdb=" CD PRO A 361 " pdb=" CG PRO A 361 " ideal model delta sigma weight residual 103.20 75.56 27.64 1.50e+00 4.44e-01 3.40e+02 angle pdb=" CA PRO A 360 " pdb=" N PRO A 360 " pdb=" CD PRO A 360 " ideal model delta sigma weight residual 112.00 87.52 24.48 1.40e+00 5.10e-01 3.06e+02 ... (remaining 8438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.82: 3317 18.82 - 37.65: 336 37.65 - 56.47: 96 56.47 - 75.29: 21 75.29 - 94.12: 4 Dihedral angle restraints: 3774 sinusoidal: 1542 harmonic: 2232 Sorted by residual: dihedral pdb=" N PRO A 361 " pdb=" CG PRO A 361 " pdb=" CD PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sinusoidal sigma weight residual -30.00 -116.67 86.67 1 1.50e+01 4.44e-03 4.02e+01 dihedral pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " pdb=" CG PRO A 361 " pdb=" CD PRO A 361 " ideal model delta sinusoidal sigma weight residual -38.00 -132.12 94.12 1 2.00e+01 2.50e-03 2.57e+01 dihedral pdb=" N PRO A 509 " pdb=" CG PRO A 509 " pdb=" CD PRO A 509 " pdb=" CB PRO A 509 " ideal model delta sinusoidal sigma weight residual -30.00 -82.93 52.93 1 1.50e+01 4.44e-03 1.69e+01 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 653 0.034 - 0.067: 193 0.067 - 0.101: 59 0.101 - 0.135: 32 0.135 - 0.168: 2 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA TRP A 336 " pdb=" N TRP A 336 " pdb=" C TRP A 336 " pdb=" CB TRP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB ILE A 273 " pdb=" CA ILE A 273 " pdb=" CG1 ILE A 273 " pdb=" CG2 ILE A 273 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA VAL B 141 " pdb=" N VAL B 141 " pdb=" C VAL B 141 " pdb=" CB VAL B 141 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 936 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 359 " -0.144 5.00e-02 4.00e+02 1.91e-01 5.85e+01 pdb=" N PRO A 360 " 0.329 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 508 " 0.048 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO A 509 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 483 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 484 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 484 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 484 " -0.026 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 686 2.75 - 3.29: 5833 3.29 - 3.82: 10759 3.82 - 4.36: 13544 4.36 - 4.90: 22165 Nonbonded interactions: 52987 Sorted by model distance: nonbonded pdb=" OE2 GLU A 67 " pdb=" NH2 ARG B 13 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP A 401 " pdb=" OG SER A 403 " model vdw 2.224 3.040 nonbonded pdb=" O GLN A 554 " pdb=" O HOH A 601 " model vdw 2.263 3.040 nonbonded pdb=" O ILE B 126 " pdb=" O HOH B 501 " model vdw 2.268 3.040 nonbonded pdb=" O VAL B 106 " pdb=" O HOH B 502 " model vdw 2.271 3.040 ... (remaining 52982 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 114.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.554 6214 Z= 0.281 Angle : 1.147 59.539 8443 Z= 0.577 Chirality : 0.040 0.168 939 Planarity : 0.008 0.191 1094 Dihedral : 16.812 94.116 2334 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.98 % Allowed : 17.23 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 764 helix: 1.72 (0.27), residues: 364 sheet: 1.30 (0.52), residues: 104 loop : -0.84 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 PHE 0.009 0.001 PHE A 304 TYR 0.011 0.001 TYR A 495 ARG 0.010 0.001 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.14535 ( 322) hydrogen bonds : angle 5.53745 ( 987) covalent geometry : bond 0.01036 ( 6214) covalent geometry : angle 1.14694 ( 8443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.730 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 1.1957 time to fit residues: 109.7988 Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 502 ASN B 75 ASN B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130581 restraints weight = 5722.861| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.17 r_work: 0.3224 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6214 Z= 0.108 Angle : 0.526 13.777 8443 Z= 0.278 Chirality : 0.040 0.172 939 Planarity : 0.005 0.084 1094 Dihedral : 5.169 28.977 928 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.23 % Favored : 97.64 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 764 helix: 1.97 (0.27), residues: 373 sheet: 1.24 (0.51), residues: 104 loop : -0.69 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 223 PHE 0.018 0.001 PHE A 392 TYR 0.015 0.001 TYR B 155 ARG 0.008 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 322) hydrogen bonds : angle 4.02745 ( 987) covalent geometry : bond 0.00223 ( 6214) covalent geometry : angle 0.52595 ( 8443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7422 (tmm160) cc_final: 0.7070 (ttp80) REVERT: A 267 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6862 (mt-10) REVERT: A 292 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6487 (tt0) REVERT: B 42 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7651 (t0) outliers start: 16 outliers final: 5 residues processed: 85 average time/residue: 2.2500 time to fit residues: 202.3770 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 332 GLN A 542 GLN B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126288 restraints weight = 5846.063| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.18 r_work: 0.3129 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6214 Z= 0.129 Angle : 0.529 7.614 8443 Z= 0.282 Chirality : 0.042 0.176 939 Planarity : 0.005 0.043 1094 Dihedral : 4.668 24.050 915 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.05 % Allowed : 14.94 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 764 helix: 1.96 (0.27), residues: 371 sheet: 1.31 (0.50), residues: 105 loop : -0.73 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 223 PHE 0.013 0.002 PHE B 340 TYR 0.010 0.002 TYR B 155 ARG 0.007 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 322) hydrogen bonds : angle 3.98227 ( 987) covalent geometry : bond 0.00268 ( 6214) covalent geometry : angle 0.52930 ( 8443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: A 292 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: A 334 LEU cc_start: 0.8630 (mt) cc_final: 0.8425 (mt) REVERT: B 72 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7725 (ttt-90) outliers start: 20 outliers final: 11 residues processed: 79 average time/residue: 1.5839 time to fit residues: 131.0427 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.150702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126253 restraints weight = 5894.464| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.23 r_work: 0.3143 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6214 Z= 0.123 Angle : 0.512 7.643 8443 Z= 0.273 Chirality : 0.042 0.178 939 Planarity : 0.004 0.037 1094 Dihedral : 4.588 22.310 915 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.35 % Allowed : 15.24 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.30), residues: 764 helix: 1.93 (0.27), residues: 371 sheet: 1.29 (0.50), residues: 105 loop : -0.73 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 PHE 0.012 0.001 PHE B 340 TYR 0.011 0.002 TYR B 155 ARG 0.005 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 322) hydrogen bonds : angle 3.91275 ( 987) covalent geometry : bond 0.00257 ( 6214) covalent geometry : angle 0.51161 ( 8443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 259 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7136 (ttm110) REVERT: A 292 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: B 42 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 72 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7712 (ttt-90) outliers start: 22 outliers final: 11 residues processed: 80 average time/residue: 2.7748 time to fit residues: 232.8594 Evaluate side-chains 83 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.150862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126964 restraints weight = 5922.716| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.17 r_work: 0.3119 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6214 Z= 0.118 Angle : 0.503 7.600 8443 Z= 0.269 Chirality : 0.042 0.177 939 Planarity : 0.004 0.037 1094 Dihedral : 4.511 21.179 915 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 15.40 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 764 helix: 1.97 (0.27), residues: 371 sheet: 1.25 (0.49), residues: 105 loop : -0.70 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 PHE 0.012 0.001 PHE B 340 TYR 0.011 0.002 TYR B 155 ARG 0.006 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 322) hydrogen bonds : angle 3.86503 ( 987) covalent geometry : bond 0.00244 ( 6214) covalent geometry : angle 0.50278 ( 8443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7244 (ttm110) REVERT: A 292 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: B 42 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7846 (t0) REVERT: B 72 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7700 (ttt-90) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 1.4515 time to fit residues: 123.1411 Evaluate side-chains 80 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126813 restraints weight = 5854.250| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.15 r_work: 0.3140 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6214 Z= 0.110 Angle : 0.488 7.462 8443 Z= 0.261 Chirality : 0.041 0.171 939 Planarity : 0.004 0.041 1094 Dihedral : 4.375 19.349 915 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.44 % Allowed : 16.16 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 764 helix: 2.03 (0.27), residues: 371 sheet: 1.23 (0.49), residues: 105 loop : -0.65 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS B 198 PHE 0.011 0.001 PHE B 340 TYR 0.011 0.001 TYR B 155 ARG 0.009 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 322) hydrogen bonds : angle 3.80239 ( 987) covalent geometry : bond 0.00225 ( 6214) covalent geometry : angle 0.48783 ( 8443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7436 (tmm160) cc_final: 0.7092 (ttp80) REVERT: A 292 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: B 72 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7694 (ttt-90) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 1.5434 time to fit residues: 124.0992 Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125908 restraints weight = 5834.859| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.20 r_work: 0.3146 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6214 Z= 0.121 Angle : 0.511 7.600 8443 Z= 0.273 Chirality : 0.042 0.177 939 Planarity : 0.005 0.040 1094 Dihedral : 4.433 20.246 914 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.90 % Allowed : 16.31 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 764 helix: 1.98 (0.27), residues: 371 sheet: 1.26 (0.49), residues: 105 loop : -0.71 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.008 0.001 HIS A 471 PHE 0.012 0.001 PHE B 340 TYR 0.011 0.002 TYR B 155 ARG 0.009 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 322) hydrogen bonds : angle 3.84284 ( 987) covalent geometry : bond 0.00253 ( 6214) covalent geometry : angle 0.51116 ( 8443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7381 (mm-30) REVERT: A 259 ARG cc_start: 0.7298 (tmm160) cc_final: 0.6982 (ttp80) REVERT: A 292 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: B 19 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8169 (p0) REVERT: B 72 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7681 (ttt-90) outliers start: 19 outliers final: 11 residues processed: 81 average time/residue: 1.4699 time to fit residues: 124.7273 Evaluate side-chains 81 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125970 restraints weight = 5836.439| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.26 r_work: 0.3150 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6214 Z= 0.122 Angle : 0.515 7.599 8443 Z= 0.276 Chirality : 0.042 0.180 939 Planarity : 0.005 0.042 1094 Dihedral : 4.469 20.453 914 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.90 % Allowed : 16.62 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 764 helix: 1.95 (0.27), residues: 371 sheet: 1.28 (0.49), residues: 105 loop : -0.70 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.009 0.001 HIS A 471 PHE 0.013 0.001 PHE B 340 TYR 0.010 0.002 TYR B 155 ARG 0.010 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 322) hydrogen bonds : angle 3.84651 ( 987) covalent geometry : bond 0.00258 ( 6214) covalent geometry : angle 0.51538 ( 8443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7373 (mm-30) REVERT: A 259 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6976 (ttp80) REVERT: A 292 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: B 19 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8173 (p0) REVERT: B 72 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7671 (ttt-90) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 1.6356 time to fit residues: 134.0199 Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 50 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.127137 restraints weight = 5934.654| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.22 r_work: 0.3143 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6214 Z= 0.104 Angle : 0.480 7.362 8443 Z= 0.258 Chirality : 0.041 0.168 939 Planarity : 0.004 0.041 1094 Dihedral : 4.258 17.729 914 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.44 % Allowed : 16.92 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 764 helix: 2.03 (0.27), residues: 373 sheet: 1.26 (0.49), residues: 105 loop : -0.65 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.011 0.001 HIS A 471 PHE 0.010 0.001 PHE A 540 TYR 0.011 0.001 TYR B 155 ARG 0.010 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 322) hydrogen bonds : angle 3.76440 ( 987) covalent geometry : bond 0.00209 ( 6214) covalent geometry : angle 0.47998 ( 8443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 259 ARG cc_start: 0.7312 (tmm160) cc_final: 0.6932 (ttp80) REVERT: A 263 THR cc_start: 0.8560 (m) cc_final: 0.8322 (m) REVERT: A 292 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: B 19 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 72 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7639 (ttt-90) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 1.5332 time to fit residues: 128.4245 Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.149711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125686 restraints weight = 5942.639| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.24 r_work: 0.3167 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6214 Z= 0.125 Angle : 0.519 7.577 8443 Z= 0.278 Chirality : 0.042 0.179 939 Planarity : 0.005 0.041 1094 Dihedral : 4.402 19.666 914 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.13 % Allowed : 17.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.30), residues: 764 helix: 1.99 (0.27), residues: 371 sheet: 1.24 (0.49), residues: 105 loop : -0.66 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.011 0.001 HIS A 471 PHE 0.013 0.001 PHE B 340 TYR 0.011 0.002 TYR B 155 ARG 0.010 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 322) hydrogen bonds : angle 3.82904 ( 987) covalent geometry : bond 0.00267 ( 6214) covalent geometry : angle 0.51896 ( 8443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7330 (mm-30) REVERT: A 259 ARG cc_start: 0.7257 (tmm160) cc_final: 0.6888 (ttp80) REVERT: A 263 THR cc_start: 0.8472 (m) cc_final: 0.8230 (m) REVERT: A 292 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: B 19 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (p0) REVERT: B 72 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7652 (ttt-90) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 1.3957 time to fit residues: 114.2960 Evaluate side-chains 81 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.0050 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 57 optimal weight: 0.0010 chunk 69 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.156129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132168 restraints weight = 5962.403| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.25 r_work: 0.3234 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6214 Z= 0.092 Angle : 0.450 7.050 8443 Z= 0.243 Chirality : 0.040 0.156 939 Planarity : 0.004 0.043 1094 Dihedral : 3.989 16.443 914 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.09 % Favored : 97.77 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.30), residues: 764 helix: 2.16 (0.27), residues: 373 sheet: 1.31 (0.49), residues: 105 loop : -0.57 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.008 0.001 HIS A 471 PHE 0.008 0.001 PHE A 304 TYR 0.011 0.001 TYR B 155 ARG 0.010 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 322) hydrogen bonds : angle 3.65636 ( 987) covalent geometry : bond 0.00182 ( 6214) covalent geometry : angle 0.44981 ( 8443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6305.90 seconds wall clock time: 113 minutes 35.66 seconds (6815.66 seconds total)