Starting phenix.real_space_refine on Mon Apr 28 19:32:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5w_38954/04_2025/8y5w_38954.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Na 4 4.78 5 C 5382 2.51 5 N 1218 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8015 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4010 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 481} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3991 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' NA': 2, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' NA': 2, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.18, per 1000 atoms: 0.65 Number of scatterers: 8015 At special positions: 0 Unit cell: (87.927, 94.6262, 113.049, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Na 4 11.00 O 1356 8.00 N 1218 7.00 C 5382 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 1 sheets defined 78.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.817A pdb=" N ILE A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.633A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.661A pdb=" N VAL A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 61 through 69 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.560A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 119 through 136 removed outlier: 3.595A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 161 Proline residue: A 149 - end of helix removed outlier: 3.504A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.723A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.681A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.590A pdb=" N LYS A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 341 removed outlier: 3.802A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.738A pdb=" N LEU A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 432 through 452 Processing helix chain 'A' and resid 453 through 462 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.575A pdb=" N ILE A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 497 through 507 Proline residue: A 503 - end of helix removed outlier: 4.069A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.799A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 3.947A pdb=" N SER A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.507A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.662A pdb=" N MET A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 10 through 23 removed outlier: 3.739A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.721A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 removed outlier: 4.181A pdb=" N LYS B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 61 through 69 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.585A pdb=" N ALA B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.572A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.539A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.518A pdb=" N VAL B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.648A pdb=" N LEU B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 254' Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 282 through 308 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.805A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.535A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.595A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 452 Processing helix chain 'B' and resid 453 through 461 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 489 through 508 Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.764A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.793A pdb=" N SER B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.554A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 3.747A pdb=" N ALA B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.827A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1479 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: 2.27 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2304 1.34 - 1.46: 2136 1.46 - 1.58: 3717 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 8244 Sorted by residual: bond pdb=" C VAL B 574 " pdb=" N PRO B 575 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.85e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" O2 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.456 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" O4 SO4 B 903 " pdb=" S SO4 B 903 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" O4 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.20e+00 ... (remaining 8239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 11004 1.68 - 3.37: 211 3.37 - 5.05: 31 5.05 - 6.73: 17 6.73 - 8.42: 3 Bond angle restraints: 11266 Sorted by residual: angle pdb=" CB MET B 315 " pdb=" CG MET B 315 " pdb=" SD MET B 315 " ideal model delta sigma weight residual 112.70 121.12 -8.42 3.00e+00 1.11e-01 7.87e+00 angle pdb=" C SER A 429 " pdb=" N PHE A 430 " pdb=" CA PHE A 430 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" C LEU B 60 " pdb=" N LEU B 61 " pdb=" CA LEU B 61 " ideal model delta sigma weight residual 120.09 123.38 -3.29 1.25e+00 6.40e-01 6.92e+00 angle pdb=" N VAL A 574 " pdb=" CA VAL A 574 " pdb=" C VAL A 574 " ideal model delta sigma weight residual 108.88 114.45 -5.57 2.16e+00 2.14e-01 6.64e+00 angle pdb=" C LEU B 30 " pdb=" N HIS B 31 " pdb=" CA HIS B 31 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.09e+00 ... (remaining 11261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4464 16.23 - 32.46: 256 32.46 - 48.69: 39 48.69 - 64.92: 8 64.92 - 81.15: 7 Dihedral angle restraints: 4774 sinusoidal: 1792 harmonic: 2982 Sorted by residual: dihedral pdb=" CA VAL B 510 " pdb=" C VAL B 510 " pdb=" N ASN B 511 " pdb=" CA ASN B 511 " ideal model delta harmonic sigma weight residual 180.00 152.43 27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL A 29 " pdb=" C VAL A 29 " pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ARG A 364 " pdb=" C ARG A 364 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " ideal model delta harmonic sigma weight residual -180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 4771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 859 0.035 - 0.070: 388 0.070 - 0.105: 87 0.105 - 0.141: 13 0.141 - 0.176: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE B 416 " pdb=" N PHE B 416 " pdb=" C PHE B 416 " pdb=" CB PHE B 416 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA VAL B 29 " pdb=" N VAL B 29 " pdb=" C VAL B 29 " pdb=" CB VAL B 29 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB THR B 50 " pdb=" CA THR B 50 " pdb=" OG1 THR B 50 " pdb=" CG2 THR B 50 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1346 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 25 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 535 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 365 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 366 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " 0.022 5.00e-02 4.00e+02 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 215 2.71 - 3.26: 8400 3.26 - 3.81: 13416 3.81 - 4.35: 16954 4.35 - 4.90: 28735 Nonbonded interactions: 67720 Sorted by model distance: nonbonded pdb=" NE1 TRP A 424 " pdb=" OD1 ASP B 434 " model vdw 2.168 3.120 nonbonded pdb=" OH TYR A 345 " pdb=" O ALA A 401 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR B 582 " pdb=" O PRO B 587 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 582 " pdb=" O PRO A 587 " model vdw 2.259 3.040 nonbonded pdb=" O ILE B 250 " pdb=" OG1 THR B 254 " model vdw 2.266 3.040 ... (remaining 67715 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 316 or resid 323 through 588 or resid 602)) selection = (chain 'B' and (resid 2 through 161 or resid 230 through 588 or resid 902)) } 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: 1.750 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: 21.510 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.003 0.042 8244 Z= 0.152 Angle : 0.641 8.418 11266 Z= 0.369 Chirality : 0.040 0.176 1349 Planarity : 0.005 0.049 1340 Dihedral : 11.206 81.152 2838 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 1009 helix: 1.26 (0.20), residues: 715 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.003 0.001 HIS B 544 PHE 0.024 0.001 PHE B 416 TYR 0.014 0.001 TYR B 81 ARG 0.002 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.17606 ( 499) hydrogen bonds : angle 5.49001 ( 1479) covalent geometry : bond 0.00308 ( 8244) covalent geometry : angle 0.64086 (11266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.815 Fit side-chains REVERT: A 11 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7698 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.0522 time to fit residues: 121.9701 Evaluate side-chains 88 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 338 GLN A 460 ASN ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122375 restraints weight = 9761.067| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.82 r_work: 0.3261 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8244 Z= 0.132 Angle : 0.581 7.448 11266 Z= 0.299 Chirality : 0.040 0.136 1349 Planarity : 0.005 0.046 1340 Dihedral : 4.459 27.519 1062 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 1.37 % Allowed : 6.74 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.28), residues: 1009 helix: 1.43 (0.20), residues: 738 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.003 0.001 HIS B 544 PHE 0.016 0.001 PHE A 287 TYR 0.010 0.001 TYR B 81 ARG 0.003 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 499) hydrogen bonds : angle 4.12268 ( 1479) covalent geometry : bond 0.00288 ( 8244) covalent geometry : angle 0.58142 (11266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.879 Fit side-chains REVERT: A 11 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7777 (mtm-85) REVERT: A 576 MET cc_start: 0.8382 (ptp) cc_final: 0.8090 (ptt) REVERT: B 123 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 336 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: B 447 ASP cc_start: 0.8617 (m-30) cc_final: 0.8388 (m-30) REVERT: B 483 SER cc_start: 0.8827 (t) cc_final: 0.8626 (m) REVERT: B 484 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8564 (mp) outliers start: 12 outliers final: 2 residues processed: 99 average time/residue: 1.0831 time to fit residues: 114.9750 Evaluate side-chains 94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 484 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 338 GLN A 460 ASN ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.154633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121186 restraints weight = 9845.604| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.84 r_work: 0.3249 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8244 Z= 0.130 Angle : 0.572 7.810 11266 Z= 0.292 Chirality : 0.040 0.127 1349 Planarity : 0.005 0.044 1340 Dihedral : 4.448 28.175 1062 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 1.71 % Allowed : 9.03 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 1009 helix: 1.69 (0.20), residues: 725 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 424 HIS 0.003 0.001 HIS B 544 PHE 0.016 0.001 PHE A 287 TYR 0.010 0.001 TYR B 81 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 499) hydrogen bonds : angle 3.88335 ( 1479) covalent geometry : bond 0.00303 ( 8244) covalent geometry : angle 0.57192 (11266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7767 (mtm-85) REVERT: A 474 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 127 PHE cc_start: 0.7597 (m-80) cc_final: 0.7349 (m-80) REVERT: B 336 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 447 ASP cc_start: 0.8701 (m-30) cc_final: 0.8457 (m-30) REVERT: B 484 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8569 (mp) outliers start: 15 outliers final: 4 residues processed: 100 average time/residue: 1.1223 time to fit residues: 120.3715 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 484 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121755 restraints weight = 9776.356| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.82 r_work: 0.2981 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8244 Z= 0.122 Angle : 0.560 7.980 11266 Z= 0.285 Chirality : 0.040 0.126 1349 Planarity : 0.005 0.044 1340 Dihedral : 4.400 28.320 1062 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 1.37 % Allowed : 10.97 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 1009 helix: 1.79 (0.20), residues: 725 sheet: None (None), residues: 0 loop : -1.85 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 424 HIS 0.003 0.001 HIS B 544 PHE 0.014 0.001 PHE A 287 TYR 0.008 0.001 TYR B 514 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 499) hydrogen bonds : angle 3.78085 ( 1479) covalent geometry : bond 0.00282 ( 8244) covalent geometry : angle 0.55978 (11266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.924 Fit side-chains REVERT: A 11 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7616 (mtm-85) REVERT: A 566 MET cc_start: 0.7447 (mmm) cc_final: 0.7151 (mmm) REVERT: B 11 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8246 (ptt-90) REVERT: B 336 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: B 447 ASP cc_start: 0.8669 (m-30) cc_final: 0.8414 (m-30) REVERT: B 484 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8469 (mp) outliers start: 12 outliers final: 4 residues processed: 98 average time/residue: 1.1214 time to fit residues: 117.5086 Evaluate side-chains 93 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 484 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118276 restraints weight = 9655.669| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.82 r_work: 0.3209 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8244 Z= 0.162 Angle : 0.602 8.600 11266 Z= 0.306 Chirality : 0.042 0.172 1349 Planarity : 0.005 0.044 1340 Dihedral : 4.538 29.353 1062 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 1.94 % Allowed : 11.31 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 1009 helix: 1.69 (0.20), residues: 727 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.005 0.001 HIS B 105 PHE 0.017 0.001 PHE A 287 TYR 0.013 0.001 TYR A 10 ARG 0.001 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 499) hydrogen bonds : angle 3.81607 ( 1479) covalent geometry : bond 0.00398 ( 8244) covalent geometry : angle 0.60223 (11266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.867 Fit side-chains REVERT: A 11 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7809 (mtm-85) REVERT: A 474 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 50 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7548 (p) REVERT: B 336 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 447 ASP cc_start: 0.8727 (m-30) cc_final: 0.8491 (m-30) REVERT: B 484 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 17 outliers final: 7 residues processed: 107 average time/residue: 1.0308 time to fit residues: 118.5928 Evaluate side-chains 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN B 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117463 restraints weight = 9705.573| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.82 r_work: 0.3194 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8244 Z= 0.164 Angle : 0.603 8.665 11266 Z= 0.308 Chirality : 0.042 0.150 1349 Planarity : 0.005 0.045 1340 Dihedral : 4.618 29.748 1062 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 2.06 % Allowed : 11.31 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.28), residues: 1009 helix: 1.63 (0.20), residues: 733 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 424 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.001 PHE A 287 TYR 0.012 0.001 TYR A 10 ARG 0.003 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 499) hydrogen bonds : angle 3.80889 ( 1479) covalent geometry : bond 0.00403 ( 8244) covalent geometry : angle 0.60333 (11266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.969 Fit side-chains REVERT: A 11 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7840 (mtm-85) REVERT: A 327 LYS cc_start: 0.7493 (mptt) cc_final: 0.7017 (mptt) REVERT: A 474 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (mp) REVERT: B 50 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7579 (p) REVERT: B 336 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 447 ASP cc_start: 0.8703 (m-30) cc_final: 0.8470 (m-30) REVERT: B 484 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8646 (mp) outliers start: 18 outliers final: 6 residues processed: 107 average time/residue: 1.0369 time to fit residues: 119.1765 Evaluate side-chains 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118715 restraints weight = 9754.280| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.82 r_work: 0.3212 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8244 Z= 0.136 Angle : 0.578 9.907 11266 Z= 0.295 Chirality : 0.041 0.145 1349 Planarity : 0.005 0.045 1340 Dihedral : 4.536 28.700 1062 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 2.63 % Allowed : 10.51 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 1009 helix: 1.77 (0.20), residues: 727 sheet: None (None), residues: 0 loop : -1.68 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 424 HIS 0.003 0.001 HIS B 544 PHE 0.016 0.001 PHE A 287 TYR 0.018 0.001 TYR A 345 ARG 0.006 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 499) hydrogen bonds : angle 3.73232 ( 1479) covalent geometry : bond 0.00325 ( 8244) covalent geometry : angle 0.57783 (11266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.899 Fit side-chains REVERT: A 11 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: A 327 LYS cc_start: 0.7429 (mptt) cc_final: 0.7229 (mptt) REVERT: A 331 GLU cc_start: 0.7780 (tp30) cc_final: 0.7303 (tp30) REVERT: A 474 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 315 MET cc_start: 0.2717 (mmm) cc_final: 0.0328 (pmt) REVERT: B 336 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: B 338 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7775 (tp40) REVERT: B 447 ASP cc_start: 0.8692 (m-30) cc_final: 0.8455 (m-30) REVERT: B 484 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 549 ASP cc_start: 0.7586 (m-30) cc_final: 0.7327 (m-30) outliers start: 23 outliers final: 10 residues processed: 109 average time/residue: 1.0194 time to fit residues: 119.3333 Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119177 restraints weight = 9888.572| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.83 r_work: 0.3219 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8244 Z= 0.131 Angle : 0.574 8.572 11266 Z= 0.292 Chirality : 0.040 0.132 1349 Planarity : 0.005 0.046 1340 Dihedral : 4.490 28.741 1062 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 2.40 % Allowed : 10.97 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 1009 helix: 1.77 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 424 HIS 0.003 0.001 HIS B 544 PHE 0.013 0.001 PHE B 85 TYR 0.016 0.001 TYR A 345 ARG 0.004 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 499) hydrogen bonds : angle 3.69450 ( 1479) covalent geometry : bond 0.00311 ( 8244) covalent geometry : angle 0.57434 (11266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.741 Fit side-chains REVERT: A 11 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7813 (mtm-85) REVERT: A 286 THR cc_start: 0.9232 (p) cc_final: 0.9028 (t) REVERT: A 327 LYS cc_start: 0.7414 (mptt) cc_final: 0.7210 (mptt) REVERT: A 331 GLU cc_start: 0.7766 (tp30) cc_final: 0.7346 (tp30) REVERT: A 474 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 272 ARG cc_start: 0.9028 (ttt180) cc_final: 0.8648 (ttt-90) REVERT: B 315 MET cc_start: 0.2717 (mmm) cc_final: 0.0383 (pmt) REVERT: B 336 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 447 ASP cc_start: 0.8692 (m-30) cc_final: 0.8481 (m-30) REVERT: B 484 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 549 ASP cc_start: 0.7569 (m-30) cc_final: 0.7306 (m-30) outliers start: 21 outliers final: 10 residues processed: 111 average time/residue: 1.0550 time to fit residues: 125.4963 Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 62 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121775 restraints weight = 9999.087| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.85 r_work: 0.3014 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8244 Z= 0.113 Angle : 0.551 8.272 11266 Z= 0.281 Chirality : 0.040 0.131 1349 Planarity : 0.005 0.046 1340 Dihedral : 4.365 27.552 1062 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 1.71 % Allowed : 11.89 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 1009 helix: 1.89 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.72 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 424 HIS 0.002 0.001 HIS B 544 PHE 0.014 0.001 PHE B 430 TYR 0.015 0.001 TYR A 345 ARG 0.004 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 499) hydrogen bonds : angle 3.62001 ( 1479) covalent geometry : bond 0.00250 ( 8244) covalent geometry : angle 0.55093 (11266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.930 Fit side-chains REVERT: A 11 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: A 331 GLU cc_start: 0.7729 (tp30) cc_final: 0.7303 (tp30) REVERT: A 474 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 338 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: B 447 ASP cc_start: 0.8650 (m-30) cc_final: 0.8400 (m-30) REVERT: B 484 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 549 ASP cc_start: 0.7518 (m-30) cc_final: 0.7226 (m-30) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 1.0648 time to fit residues: 121.6750 Evaluate side-chains 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122841 restraints weight = 9804.078| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.82 r_work: 0.3270 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8244 Z= 0.112 Angle : 0.555 11.334 11266 Z= 0.280 Chirality : 0.040 0.162 1349 Planarity : 0.005 0.047 1340 Dihedral : 4.272 27.458 1062 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.03 % Allowed : 13.03 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.28), residues: 1009 helix: 1.96 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.64 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 424 HIS 0.002 0.001 HIS B 86 PHE 0.013 0.001 PHE B 287 TYR 0.016 0.001 TYR A 345 ARG 0.007 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 499) hydrogen bonds : angle 3.58824 ( 1479) covalent geometry : bond 0.00250 ( 8244) covalent geometry : angle 0.55545 (11266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: A 331 GLU cc_start: 0.7732 (tp30) cc_final: 0.7350 (tp30) REVERT: A 536 ASN cc_start: 0.8499 (m-40) cc_final: 0.8213 (m110) REVERT: B 338 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7776 (tp40) REVERT: B 447 ASP cc_start: 0.8679 (m-30) cc_final: 0.8451 (m-30) REVERT: B 484 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8608 (mp) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 1.1027 time to fit residues: 128.0570 Evaluate side-chains 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 460 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120708 restraints weight = 9769.062| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3238 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8244 Z= 0.131 Angle : 0.580 11.282 11266 Z= 0.292 Chirality : 0.041 0.181 1349 Planarity : 0.005 0.046 1340 Dihedral : 4.333 27.653 1062 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 1.26 % Allowed : 13.26 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 1009 helix: 1.90 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.70 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 372 HIS 0.003 0.001 HIS B 86 PHE 0.013 0.001 PHE B 85 TYR 0.022 0.001 TYR A 514 ARG 0.005 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 499) hydrogen bonds : angle 3.62619 ( 1479) covalent geometry : bond 0.00311 ( 8244) covalent geometry : angle 0.57987 (11266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6060.99 seconds wall clock time: 104 minutes 51.51 seconds (6291.51 seconds total)