Starting phenix.real_space_refine on Wed Feb 12 13:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5w_38954/02_2025/8y5w_38954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5w_38954/02_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_38954/02_2025/8y5w_38954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5w_38954/02_2025/8y5w_38954.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5w_38954/02_2025/8y5w_38954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5w_38954/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.09, per 1000 atoms: 0.64 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 1.1 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: 0.70 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: 2.16 Time building geometry restraints manager: 2.21 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: 1.430 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.470 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.580 ------------------------------------------------------------------------------- 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= 0.198 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 *********************** 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 : 0.906 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: 1.0333 time to fit residues: 119.9953 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 : 0.836 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122409 restraints weight = 9761.064| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.82 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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= 0.185 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 *********************** 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 : 0.887 Fit side-chains REVERT: A 11 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: A 576 MET cc_start: 0.8379 (ptp) cc_final: 0.8086 (ptt) REVERT: B 123 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8343 (tt) REVERT: B 336 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 447 ASP cc_start: 0.8621 (m-30) cc_final: 0.8393 (m-30) REVERT: B 483 SER cc_start: 0.8820 (t) cc_final: 0.8620 (m) REVERT: B 484 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 12 outliers final: 2 residues processed: 99 average time/residue: 1.1124 time to fit residues: 118.1773 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 : 0.863 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 160 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 = 0.3772 r_free = 0.3772 target = 0.152299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118567 restraints weight = 9840.618| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.83 r_work: 0.3201 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8244 Z= 0.262 Angle : 0.610 7.868 11266 Z= 0.312 Chirality : 0.042 0.132 1349 Planarity : 0.005 0.044 1340 Dihedral : 4.586 28.919 1062 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 1.60 % Allowed : 9.37 % Favored : 89.03 % 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: 0.91 (0.28), residues: 1009 helix: 1.56 (0.20), residues: 723 sheet: None (None), residues: 0 loop : -1.96 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 424 HIS 0.005 0.001 HIS B 105 PHE 0.018 0.001 PHE A 287 TYR 0.012 0.001 TYR A 10 ARG 0.002 0.000 ARG A 277 *********************** 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 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.853 Fit side-chains REVERT: A 11 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7848 (mtm-85) REVERT: B 272 ARG cc_start: 0.9086 (ttt180) cc_final: 0.8840 (ttt180) REVERT: B 336 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: B 447 ASP cc_start: 0.8707 (m-30) cc_final: 0.8484 (m-30) REVERT: B 483 SER cc_start: 0.8846 (t) cc_final: 0.8646 (m) REVERT: B 484 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8588 (mp) outliers start: 14 outliers final: 5 residues processed: 98 average time/residue: 1.0678 time to fit residues: 112.2886 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 : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 480 MET 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: 0.0970 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 75 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122622 restraints weight = 9783.665| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.82 r_work: 0.3003 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1408 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= 0.157 Angle : 0.546 8.116 11266 Z= 0.279 Chirality : 0.039 0.131 1349 Planarity : 0.005 0.045 1340 Dihedral : 4.421 28.166 1062 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 1.49 % Allowed : 10.74 % Favored : 87.77 % 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: 1.23 (0.28), residues: 1009 helix: 1.80 (0.20), residues: 725 sheet: None (None), residues: 0 loop : -1.86 (0.38), residues: 284 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 0.014 0.001 PHE B 430 TYR 0.009 0.001 TYR A 345 ARG 0.002 0.000 ARG B 11 *********************** 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 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.824 Fit side-chains REVERT: A 11 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7578 (mtm-85) REVERT: A 474 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 566 MET cc_start: 0.7417 (mmm) cc_final: 0.7122 (mmm) REVERT: B 11 ARG cc_start: 0.8576 (ptp90) cc_final: 0.8270 (ptt-90) REVERT: B 336 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: B 447 ASP cc_start: 0.8663 (m-30) cc_final: 0.8407 (m-30) REVERT: B 483 SER cc_start: 0.8762 (t) cc_final: 0.8520 (m) REVERT: B 484 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8468 (mp) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 1.1225 time to fit residues: 127.1587 Evaluate side-chains 99 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 158 ILE 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: 2.9990 chunk 67 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.149703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115712 restraints weight = 9659.002| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.82 r_work: 0.3160 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8244 Z= 0.347 Angle : 0.654 8.967 11266 Z= 0.332 Chirality : 0.044 0.174 1349 Planarity : 0.005 0.045 1340 Dihedral : 4.724 30.387 1062 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 2.17 % Allowed : 11.09 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.91 (0.27), residues: 1009 helix: 1.51 (0.19), residues: 727 sheet: None (None), residues: 0 loop : -1.85 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 424 HIS 0.007 0.002 HIS B 105 PHE 0.021 0.002 PHE A 287 TYR 0.016 0.002 TYR A 10 ARG 0.003 0.000 ARG B 272 *********************** 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 115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.898 Fit side-chains REVERT: A 11 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: A 327 LYS cc_start: 0.7487 (mptt) cc_final: 0.6953 (mptt) REVERT: A 474 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 50 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 336 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: B 447 ASP cc_start: 0.8752 (m-30) cc_final: 0.8542 (m-30) REVERT: B 484 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8579 (mp) outliers start: 19 outliers final: 8 residues processed: 106 average time/residue: 1.0020 time to fit residues: 114.4639 Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 515 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 158 ILE 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: 0.8980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.151465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117966 restraints weight = 9699.487| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.81 r_work: 0.3203 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1663 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= 0.223 Angle : 0.585 8.846 11266 Z= 0.299 Chirality : 0.041 0.148 1349 Planarity : 0.005 0.046 1340 Dihedral : 4.626 29.718 1062 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 3.09 % Allowed : 10.51 % 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: 1.11 (0.28), residues: 1009 helix: 1.60 (0.19), residues: 737 sheet: None (None), residues: 0 loop : -1.70 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 424 HIS 0.004 0.001 HIS B 544 PHE 0.015 0.001 PHE A 287 TYR 0.015 0.001 TYR A 345 ARG 0.005 0.000 ARG B 272 *********************** 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 121 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.852 Fit side-chains REVERT: A 11 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: A 327 LYS cc_start: 0.7399 (mptt) cc_final: 0.6879 (mptt) REVERT: A 331 GLU cc_start: 0.7843 (tp30) cc_final: 0.7404 (tp30) REVERT: A 474 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 50 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7487 (p) REVERT: B 336 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: B 338 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7774 (tp40) REVERT: B 447 ASP cc_start: 0.8708 (m-30) cc_final: 0.8474 (m-30) REVERT: B 484 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8636 (mp) outliers start: 27 outliers final: 9 residues processed: 109 average time/residue: 1.0385 time to fit residues: 121.7636 Evaluate side-chains 109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 515 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 158 ILE 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 484 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 531 VAL 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: 2.9990 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117557 restraints weight = 9662.815| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.77 r_work: 0.3180 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8244 Z= 0.294 Angle : 0.627 9.826 11266 Z= 0.319 Chirality : 0.043 0.159 1349 Planarity : 0.005 0.047 1340 Dihedral : 4.714 30.971 1062 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 2.97 % Allowed : 10.51 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.99 (0.27), residues: 1009 helix: 1.57 (0.19), residues: 725 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 284 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 0.020 0.002 PHE A 287 TYR 0.013 0.001 TYR A 10 ARG 0.004 0.000 ARG B 272 *********************** 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 122 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.929 Fit side-chains REVERT: A 11 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: A 327 LYS cc_start: 0.7451 (mptt) cc_final: 0.6842 (mptt) REVERT: A 331 GLU cc_start: 0.7891 (tp30) cc_final: 0.7445 (tp30) REVERT: A 474 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 50 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (p) REVERT: B 315 MET cc_start: 0.2843 (mmm) cc_final: 0.0355 (pmt) REVERT: B 336 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 447 ASP cc_start: 0.8707 (m-30) cc_final: 0.8499 (m-30) REVERT: B 484 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7458 (m-30) outliers start: 26 outliers final: 9 residues processed: 111 average time/residue: 1.0309 time to fit residues: 123.7495 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 515 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 158 ILE 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 515 ILE 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118489 restraints weight = 9853.070| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.82 r_work: 0.3211 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1758 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= 0.194 Angle : 0.572 8.707 11266 Z= 0.293 Chirality : 0.040 0.135 1349 Planarity : 0.005 0.047 1340 Dihedral : 4.563 29.702 1062 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 2.40 % Allowed : 10.86 % 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: 1.25 (0.28), residues: 1009 helix: 1.68 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.61 (0.39), residues: 271 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 A 287 TYR 0.019 0.001 TYR A 345 ARG 0.005 0.000 ARG B 11 *********************** 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 : 0.839 Fit side-chains REVERT: A 331 GLU cc_start: 0.7827 (tp30) cc_final: 0.7399 (tp30) REVERT: A 474 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 315 MET cc_start: 0.2703 (mmm) cc_final: 0.0364 (pmt) REVERT: B 336 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 338 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7770 (tp40) REVERT: B 447 ASP cc_start: 0.8694 (m-30) cc_final: 0.8480 (m-30) REVERT: B 484 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8637 (mp) REVERT: B 549 ASP cc_start: 0.7602 (m-30) cc_final: 0.7340 (m-30) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 1.0822 time to fit residues: 125.5476 Evaluate side-chains 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 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 158 ILE 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 515 ILE 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: 0.0370 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119167 restraints weight = 9965.726| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.82 r_work: 0.3193 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1769 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= 0.195 Angle : 0.571 8.158 11266 Z= 0.291 Chirality : 0.040 0.134 1349 Planarity : 0.005 0.047 1340 Dihedral : 4.494 29.440 1062 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 2.51 % Allowed : 11.20 % Favored : 86.29 % 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: 1.28 (0.28), residues: 1009 helix: 1.77 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 276 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 0.012 0.001 PHE B 85 TYR 0.018 0.001 TYR A 345 ARG 0.003 0.000 ARG B 11 *********************** 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 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.906 Fit side-chains REVERT: A 331 GLU cc_start: 0.7796 (tp30) cc_final: 0.7383 (tp30) REVERT: A 474 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 338 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7786 (tp40) REVERT: B 447 ASP cc_start: 0.8700 (m-30) cc_final: 0.8483 (m-30) REVERT: B 484 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8606 (mp) REVERT: B 549 ASP cc_start: 0.7565 (m-30) cc_final: 0.7295 (m-30) outliers start: 22 outliers final: 12 residues processed: 109 average time/residue: 1.0242 time to fit residues: 120.4013 Evaluate side-chains 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 515 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 134 LEU Chi-restraints excluded: chain B residue 158 ILE 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 Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 0.0570 chunk 73 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.154026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120930 restraints weight = 9804.035| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.81 r_work: 0.3247 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8244 Z= 0.171 Angle : 0.562 11.480 11266 Z= 0.286 Chirality : 0.040 0.135 1349 Planarity : 0.005 0.048 1340 Dihedral : 4.399 28.779 1062 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 1.71 % Allowed : 12.11 % Favored : 86.17 % 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: 1.41 (0.28), residues: 1009 helix: 1.85 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 372 HIS 0.003 0.001 HIS B 544 PHE 0.015 0.001 PHE B 430 TYR 0.018 0.001 TYR A 345 ARG 0.004 0.000 ARG B 11 ********************** 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 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.964 Fit side-chains REVERT: A 267 GLU cc_start: 0.7070 (tt0) cc_final: 0.6828 (tp30) REVERT: A 331 GLU cc_start: 0.7806 (tp30) cc_final: 0.7378 (tp30) REVERT: A 474 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 315 MET cc_start: 0.2729 (mmm) cc_final: 0.0268 (pmt) REVERT: B 338 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7754 (tp40) REVERT: B 447 ASP cc_start: 0.8674 (m-30) cc_final: 0.8436 (m-30) REVERT: B 450 GLU cc_start: 0.7910 (tt0) cc_final: 0.7701 (tm-30) REVERT: B 484 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 549 ASP cc_start: 0.7487 (m-30) cc_final: 0.7217 (m-30) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.9997 time to fit residues: 116.5676 Evaluate side-chains 109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 515 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 Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.152349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118892 restraints weight = 9747.033| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.81 r_work: 0.3222 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1819 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= 0.218 Angle : 0.588 11.368 11266 Z= 0.299 Chirality : 0.041 0.134 1349 Planarity : 0.005 0.047 1340 Dihedral : 4.479 29.310 1062 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 1.83 % Allowed : 12.57 % Favored : 85.60 % 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: 1.33 (0.28), residues: 1009 helix: 1.80 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 424 HIS 0.004 0.001 HIS B 544 PHE 0.013 0.001 PHE B 85 TYR 0.018 0.001 TYR A 345 ARG 0.007 0.001 ARG B 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5721.19 seconds wall clock time: 101 minutes 42.42 seconds (6102.42 seconds total)