Starting phenix.real_space_refine on Wed Sep 17 06:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lum_63398/09_2025/9lum_63398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lum_63398/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lum_63398/09_2025/9lum_63398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lum_63398/09_2025/9lum_63398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lum_63398/09_2025/9lum_63398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lum_63398/09_2025/9lum_63398.map" } resolution = 2.66 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= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.85, per 1000 atoms: 0.29 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: 0.53 Conformation dependent library (CDL) restraints added in 346.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.23 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: 1.25 Time building geometry restraints manager: 0.72 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: 4.300 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: 0.010 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 322 TYR 0.011 0.001 TYR A 495 PHE 0.009 0.001 PHE A 304 TRP 0.014 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.01036 ( 6214) covalent geometry : angle 1.14694 ( 8443) hydrogen bonds : bond 0.14535 ( 322) hydrogen bonds : angle 5.53745 ( 987) *********************** 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 : 0.271 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.5908 time to fit residues: 53.9959 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 : 0.242 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 75 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.150246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125964 restraints weight = 5902.030| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.15 r_work: 0.3129 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6214 Z= 0.144 Angle : 0.593 13.153 8443 Z= 0.315 Chirality : 0.043 0.190 939 Planarity : 0.006 0.086 1094 Dihedral : 5.629 31.038 928 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.90 % Allowed : 15.85 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.13 (0.30), residues: 764 helix: 1.77 (0.27), residues: 371 sheet: 1.26 (0.50), residues: 105 loop : -0.81 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 258 TYR 0.011 0.002 TYR B 155 PHE 0.015 0.002 PHE A 392 TRP 0.013 0.001 TRP A 336 HIS 0.004 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6214) covalent geometry : angle 0.59260 ( 8443) hydrogen bonds : bond 0.05819 ( 322) hydrogen bonds : angle 4.22326 ( 987) *********************** 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 89 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7217 (ttm110) REVERT: A 267 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6913 (mt-10) REVERT: A 292 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: B 42 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7722 (t0) REVERT: B 72 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7684 (ttt-90) outliers start: 19 outliers final: 10 residues processed: 78 average time/residue: 0.6415 time to fit residues: 52.4277 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 : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 259 ARG 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 72 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 121 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 6 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128802 restraints weight = 5852.754| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.17 r_work: 0.3155 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1021 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= 0.105 Angle : 0.477 7.361 8443 Z= 0.257 Chirality : 0.041 0.170 939 Planarity : 0.004 0.038 1094 Dihedral : 4.561 21.590 916 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.74 % Allowed : 15.40 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.37 (0.30), residues: 764 helix: 1.97 (0.27), residues: 373 sheet: 1.36 (0.50), residues: 105 loop : -0.71 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 258 TYR 0.011 0.001 TYR B 155 PHE 0.009 0.001 PHE A 304 TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6214) covalent geometry : angle 0.47684 ( 8443) hydrogen bonds : bond 0.04416 ( 322) hydrogen bonds : angle 3.89211 ( 987) *********************** 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 91 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7445 (tmm160) cc_final: 0.7094 (ttp80) REVERT: A 292 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: A 334 LEU cc_start: 0.8650 (mt) cc_final: 0.8436 (mt) REVERT: B 72 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7707 (ttt-90) outliers start: 18 outliers final: 9 residues processed: 85 average time/residue: 0.6826 time to fit residues: 60.5471 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 210 ASP 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 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 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 = 0.3639 r_free = 0.3639 target = 0.151365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127372 restraints weight = 5877.272| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.19 r_work: 0.3128 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6214 Z= 0.116 Angle : 0.497 7.401 8443 Z= 0.266 Chirality : 0.041 0.171 939 Planarity : 0.004 0.036 1094 Dihedral : 4.484 21.124 915 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.20 % Allowed : 15.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.30), residues: 764 helix: 2.01 (0.27), residues: 371 sheet: 1.36 (0.50), residues: 105 loop : -0.69 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.011 0.001 TYR B 155 PHE 0.014 0.001 PHE A 392 TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6214) covalent geometry : angle 0.49733 ( 8443) hydrogen bonds : bond 0.04738 ( 322) hydrogen bonds : angle 3.87801 ( 987) *********************** 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 92 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 259 ARG cc_start: 0.7462 (tmm160) cc_final: 0.7099 (ttp80) REVERT: A 292 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6666 (tt0) REVERT: A 334 LEU cc_start: 0.8654 (mt) cc_final: 0.8453 (mt) REVERT: B 42 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 72 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7719 (ttt-90) outliers start: 21 outliers final: 12 residues processed: 83 average time/residue: 0.6720 time to fit residues: 58.2475 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 455 SER 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 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 9 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 542 GLN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126015 restraints weight = 5933.231| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.17 r_work: 0.3107 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1231 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= 0.131 Angle : 0.530 7.563 8443 Z= 0.282 Chirality : 0.042 0.184 939 Planarity : 0.005 0.036 1094 Dihedral : 4.627 22.610 915 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.35 % Allowed : 15.40 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.29 (0.30), residues: 764 helix: 1.91 (0.27), residues: 371 sheet: 1.23 (0.49), residues: 105 loop : -0.69 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 258 TYR 0.010 0.002 TYR B 155 PHE 0.014 0.001 PHE B 340 TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6214) covalent geometry : angle 0.53022 ( 8443) hydrogen bonds : bond 0.05262 ( 322) hydrogen bonds : angle 3.91384 ( 987) *********************** 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 88 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 292 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: B 42 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7854 (t0) REVERT: B 72 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7713 (ttt-90) outliers start: 22 outliers final: 11 residues processed: 78 average time/residue: 0.7165 time to fit residues: 58.2772 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU 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 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 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 72 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.0010 chunk 59 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.151025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127324 restraints weight = 5862.310| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.10 r_work: 0.3138 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1297 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= 0.111 Angle : 0.490 7.436 8443 Z= 0.263 Chirality : 0.041 0.174 939 Planarity : 0.004 0.036 1094 Dihedral : 4.434 19.968 915 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 16.31 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.39 (0.30), residues: 764 helix: 2.00 (0.27), residues: 371 sheet: 1.37 (0.49), residues: 103 loop : -0.69 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 258 TYR 0.011 0.001 TYR B 155 PHE 0.012 0.001 PHE A 540 TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6214) covalent geometry : angle 0.49015 ( 8443) hydrogen bonds : bond 0.04574 ( 322) hydrogen bonds : angle 3.82785 ( 987) *********************** 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 89 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7488 (mm-30) REVERT: A 70 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 102 ASN cc_start: 0.8252 (m110) cc_final: 0.8040 (t0) REVERT: A 259 ARG cc_start: 0.7421 (tmm160) cc_final: 0.7086 (ttp80) REVERT: A 292 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6680 (tt0) REVERT: B 42 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7792 (t0) REVERT: B 72 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7705 (ttt-90) outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 0.7063 time to fit residues: 59.6924 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 : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU 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 321 LYS 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 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 542 GLN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122882 restraints weight = 5881.344| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.15 r_work: 0.3092 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6214 Z= 0.182 Angle : 0.618 8.023 8443 Z= 0.327 Chirality : 0.046 0.209 939 Planarity : 0.005 0.042 1094 Dihedral : 5.079 27.991 914 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.81 % Allowed : 15.24 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.01 (0.29), residues: 764 helix: 1.64 (0.27), residues: 371 sheet: 1.21 (0.49), residues: 105 loop : -0.82 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.010 0.002 TYR A 301 PHE 0.018 0.002 PHE B 340 TRP 0.013 0.002 TRP A 580 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6214) covalent geometry : angle 0.61833 ( 8443) hydrogen bonds : bond 0.06535 ( 322) hydrogen bonds : angle 4.10866 ( 987) *********************** 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 90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: A 259 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7074 (ttm110) REVERT: A 292 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: B 42 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7750 (t0) REVERT: B 72 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7688 (ttt-90) outliers start: 25 outliers final: 12 residues processed: 80 average time/residue: 0.6789 time to fit residues: 56.7649 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 THR 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 A residue 571 THR 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 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 58 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.148265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124046 restraints weight = 5884.321| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.16 r_work: 0.3070 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6214 Z= 0.179 Angle : 0.606 7.956 8443 Z= 0.322 Chirality : 0.045 0.209 939 Planarity : 0.005 0.043 1094 Dihedral : 5.156 28.612 914 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.35 % Allowed : 16.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.29), residues: 764 helix: 1.54 (0.27), residues: 371 sheet: 1.13 (0.49), residues: 105 loop : -0.88 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 390 TYR 0.009 0.002 TYR B 247 PHE 0.018 0.002 PHE B 340 TRP 0.015 0.002 TRP A 336 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6214) covalent geometry : angle 0.60574 ( 8443) hydrogen bonds : bond 0.06276 ( 322) hydrogen bonds : angle 4.09984 ( 987) *********************** 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 85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7257 (ttm110) REVERT: A 292 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: B 42 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7864 (t0) REVERT: B 72 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7689 (ttt-90) outliers start: 22 outliers final: 12 residues processed: 78 average time/residue: 0.6933 time to fit residues: 56.6045 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 571 THR 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 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 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.151307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127300 restraints weight = 5920.861| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.25 r_work: 0.3122 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6214 Z= 0.129 Angle : 0.533 7.605 8443 Z= 0.286 Chirality : 0.042 0.187 939 Planarity : 0.005 0.038 1094 Dihedral : 4.814 24.108 914 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.74 % Allowed : 16.16 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.06 (0.29), residues: 764 helix: 1.72 (0.27), residues: 371 sheet: 1.14 (0.49), residues: 105 loop : -0.81 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.010 0.002 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.015 0.001 TRP A 336 HIS 0.012 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6214) covalent geometry : angle 0.53342 ( 8443) hydrogen bonds : bond 0.05206 ( 322) hydrogen bonds : angle 3.96839 ( 987) *********************** 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 85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7294 (mm-30) REVERT: A 292 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: B 42 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 72 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7681 (ttt-90) outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 0.7053 time to fit residues: 57.4196 Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR 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 321 LYS Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 571 THR 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 121 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 276 VAL 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 40 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 74 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128950 restraints weight = 5865.356| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.07 r_work: 0.3163 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6214 Z= 0.106 Angle : 0.480 7.229 8443 Z= 0.260 Chirality : 0.041 0.171 939 Planarity : 0.004 0.038 1094 Dihedral : 4.366 18.609 914 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 17.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.30), residues: 764 helix: 1.94 (0.27), residues: 371 sheet: 1.19 (0.49), residues: 105 loop : -0.71 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.011 0.001 TYR A 495 PHE 0.009 0.001 PHE B 238 TRP 0.015 0.001 TRP A 336 HIS 0.009 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6214) covalent geometry : angle 0.48041 ( 8443) hydrogen bonds : bond 0.04298 ( 322) hydrogen bonds : angle 3.80910 ( 987) ********************** 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 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7266 (mm-30) REVERT: A 102 ASN cc_start: 0.8168 (m110) cc_final: 0.7912 (t0) REVERT: A 259 ARG cc_start: 0.7145 (tmm160) cc_final: 0.6871 (ttp80) REVERT: A 292 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6636 (tt0) REVERT: B 72 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7665 (ttt-90) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.7371 time to fit residues: 60.0115 Evaluate side-chains 75 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 ASP Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 276 VAL 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 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.0010 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 59 optimal weight: 0.0010 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.152723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130294 restraints weight = 5893.004| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.08 r_work: 0.3175 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6214 Z= 0.102 Angle : 0.476 7.164 8443 Z= 0.257 Chirality : 0.041 0.166 939 Planarity : 0.004 0.038 1094 Dihedral : 4.239 17.066 914 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.37 % Allowed : 17.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.30), residues: 764 helix: 1.98 (0.27), residues: 373 sheet: 1.26 (0.49), residues: 105 loop : -0.66 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 258 TYR 0.010 0.001 TYR B 155 PHE 0.010 0.001 PHE A 540 TRP 0.014 0.001 TRP A 336 HIS 0.011 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 6214) covalent geometry : angle 0.47556 ( 8443) hydrogen bonds : bond 0.04165 ( 322) hydrogen bonds : angle 3.77368 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.01 seconds wall clock time: 43 minutes 23.20 seconds (2603.20 seconds total)