Starting phenix.real_space_refine on Sat Jul 4 01:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.map" model { file = "/net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jev_36200/07_2026/8jev_36200.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 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: 6 Type Number sf(0) Gaussians S 56 5.16 5 Cl 6 4.86 5 C 5780 2.51 5 N 1422 2.21 5 O 1482 1.98 5 H 8852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17598 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8795 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 533} Chain breaks: 6 Chain: "B" Number of atoms: 8795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8795 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 533} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 3} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.64, per 1000 atoms: 0.15 Number of scatterers: 17598 At special positions: 0 Unit cell: (94.86, 118.11, 97.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 6 17.00 S 56 16.00 O 1482 8.00 N 1422 7.00 C 5780 6.00 H 8852 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 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: 1.30 Conformation dependent library (CDL) restraints added in 437.5 milliseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 75.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.749A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.611A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.560A pdb=" N ILE A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.093A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.533A pdb=" N THR A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 419 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 498 through 518 Processing helix chain 'A' and resid 526 through 553 removed outlier: 3.750A pdb=" N SER A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.652A pdb=" N TYR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 586 " --> pdb=" O CYS A 582 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 602 removed outlier: 3.695A pdb=" N VAL A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.528A pdb=" N ALA A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.588A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 779 Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.749A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 3.582A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.567A pdb=" N ILE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 4.087A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.527A pdb=" N THR B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 349 through 366 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 419 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 498 through 518 removed outlier: 3.505A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 553 removed outlier: 3.748A pdb=" N SER B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.652A pdb=" N TYR B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 586 " --> pdb=" O CYS B 582 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 602 removed outlier: 3.683A pdb=" N VAL B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.529A pdb=" N ALA B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.651A pdb=" N ASN B 637 " --> pdb=" O HIS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 779 Processing helix chain 'B' and resid 797 through 805 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 761 through 763 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.544A pdb=" N THR B 786 " --> pdb=" O VAL B 762 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1797 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: 3.79 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8832 1.03 - 1.23: 39 1.23 - 1.42: 3769 1.42 - 1.61: 5098 1.61 - 1.81: 86 Bond restraints: 17824 Sorted by residual: bond pdb=" NZ LYS B 245 " pdb=" HZ3 LYS B 245 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NZ LYS A 245 " pdb=" HZ3 LYS A 245 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CA GLU A 339 " pdb=" C GLU A 339 " ideal model delta sigma weight residual 1.519 1.476 0.043 1.22e-02 6.72e+03 1.22e+01 bond pdb=" NZ LYS B 245 " pdb=" HZ1 LYS B 245 " ideal model delta sigma weight residual 0.890 0.958 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" NZ LYS B 245 " pdb=" HZ2 LYS B 245 " ideal model delta sigma weight residual 0.890 0.958 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 17819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.88: 32212 9.88 - 19.76: 4 19.76 - 29.64: 0 29.64 - 39.52: 0 39.52 - 49.40: 4 Bond angle restraints: 32220 Sorted by residual: angle pdb=" C THR A 348 " pdb=" N LEU A 349 " pdb=" H LEU A 349 " ideal model delta sigma weight residual 123.92 74.52 49.40 3.00e+00 1.11e-01 2.71e+02 angle pdb=" C THR B 348 " pdb=" N LEU B 349 " pdb=" H LEU B 349 " ideal model delta sigma weight residual 123.92 74.60 49.32 3.00e+00 1.11e-01 2.70e+02 angle pdb=" CA LEU A 349 " pdb=" N LEU A 349 " pdb=" H LEU A 349 " ideal model delta sigma weight residual 113.62 65.46 48.16 3.00e+00 1.11e-01 2.58e+02 angle pdb=" CA LEU B 349 " pdb=" N LEU B 349 " pdb=" H LEU B 349 " ideal model delta sigma weight residual 113.62 65.48 48.14 3.00e+00 1.11e-01 2.57e+02 angle pdb=" C THR B 348 " pdb=" N LEU B 349 " pdb=" CA LEU B 349 " ideal model delta sigma weight residual 122.46 140.08 -17.62 1.80e+00 3.09e-01 9.58e+01 ... (remaining 32215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7459 17.98 - 35.97: 643 35.97 - 53.95: 196 53.95 - 71.94: 55 71.94 - 89.92: 15 Dihedral angle restraints: 8368 sinusoidal: 4396 harmonic: 3972 Sorted by residual: dihedral pdb=" CA THR A 348 " pdb=" C THR A 348 " pdb=" N LEU A 349 " pdb=" CA LEU A 349 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR B 348 " pdb=" C THR B 348 " pdb=" N LEU B 349 " pdb=" CA LEU B 349 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CB GLU A 458 " pdb=" CG GLU A 458 " pdb=" CD GLU A 458 " pdb=" OE1 GLU A 458 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 8365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 867 0.034 - 0.067: 377 0.067 - 0.101: 105 0.101 - 0.135: 33 0.135 - 0.168: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA ILE B 252 " pdb=" N ILE B 252 " pdb=" C ILE B 252 " pdb=" CB ILE B 252 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO A 301 " pdb=" N PRO A 301 " pdb=" C PRO A 301 " pdb=" CB PRO A 301 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1381 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 391 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 392 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 630 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C TYR B 630 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR B 630 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 631 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 391 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO B 392 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 392 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 392 " -0.031 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 253 2.07 - 2.70: 29180 2.70 - 3.33: 53817 3.33 - 3.97: 67129 3.97 - 4.60: 107062 Nonbonded interactions: 257441 Sorted by model distance: nonbonded pdb=" H LEU B 349 " pdb=" HA LEU B 349 " model vdw 1.433 1.816 nonbonded pdb=" H LEU A 349 " pdb=" HA LEU A 349 " model vdw 1.434 1.816 nonbonded pdb=" HE1 TRP B 385 " pdb=" O GLU B 605 " model vdw 1.467 2.450 nonbonded pdb=" HE1 TRP A 385 " pdb=" O GLU A 605 " model vdw 1.468 2.450 nonbonded pdb=" H THR A 192 " pdb=" OE2 GLU A 195 " model vdw 1.514 2.450 ... (remaining 257436 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.030 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: 0.100 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 : 0.007 0.070 8974 Z= 0.309 Angle : 0.733 17.619 12182 Z= 0.407 Chirality : 0.042 0.168 1384 Planarity : 0.005 0.058 1472 Dihedral : 14.190 89.922 3124 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1084 helix: 0.43 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 802 TYR 0.024 0.002 TYR A 211 PHE 0.012 0.002 PHE A 775 TRP 0.023 0.002 TRP A 93 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.31 ( 8972) covalent geometry : angle 0.73268 / 0.41 (12178) SS BOND : bond 0.00478 / 0.24 ( 2) SS BOND : angle 1.35901 / 0.83 ( 4) hydrogen bonds : bond 0.14677 / 10.39 ( 608) hydrogen bonds : angle 7.06584 / 5.18 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.6851 (t80) cc_final: 0.6328 (t80) REVERT: A 215 ILE cc_start: 0.7895 (mt) cc_final: 0.7619 (mt) REVERT: A 658 MET cc_start: 0.7335 (ptm) cc_final: 0.7030 (ttp) REVERT: A 757 MET cc_start: 0.0200 (ptt) cc_final: -0.0225 (mmt) REVERT: B 200 GLN cc_start: 0.7195 (tt0) cc_final: 0.6828 (mm-40) REVERT: B 215 ILE cc_start: 0.7907 (mt) cc_final: 0.7581 (mt) REVERT: B 457 LYS cc_start: 0.7862 (mttm) cc_final: 0.7574 (mttm) REVERT: B 658 MET cc_start: 0.7500 (ptm) cc_final: 0.7038 (ttp) REVERT: B 757 MET cc_start: 0.0341 (ttp) cc_final: -0.0130 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2188 time to fit residues: 54.6115 Evaluate side-chains 128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.188080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145550 restraints weight = 30361.532| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.53 r_work: 0.3757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8974 Z= 0.161 Angle : 0.600 17.490 12182 Z= 0.322 Chirality : 0.038 0.147 1384 Planarity : 0.005 0.052 1472 Dihedral : 4.234 16.534 1190 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 0.88 % Allowed : 5.04 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1084 helix: 0.97 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.015 0.001 TYR B 211 PHE 0.011 0.001 PHE B 775 TRP 0.010 0.001 TRP A 555 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8972) covalent geometry : angle 0.59941 / 0.32 (12178) SS BOND : bond 0.00285 / 0.14 ( 2) SS BOND : angle 1.40156 / 0.88 ( 4) hydrogen bonds : bond 0.05222 / 3.50 ( 608) hydrogen bonds : angle 5.19882 / 3.79 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7139 (ttt180) cc_final: 0.6900 (ttm170) REVERT: A 123 TYR cc_start: 0.6617 (t80) cc_final: 0.6192 (t80) REVERT: A 168 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7715 (p0) REVERT: A 215 ILE cc_start: 0.7856 (mt) cc_final: 0.7544 (mt) REVERT: A 611 MET cc_start: 0.7256 (tpt) cc_final: 0.6835 (tpp) REVERT: A 635 ARG cc_start: 0.7855 (mmp80) cc_final: 0.7472 (ttm110) REVERT: A 658 MET cc_start: 0.7557 (ptm) cc_final: 0.7117 (ttp) REVERT: A 757 MET cc_start: -0.0052 (ptt) cc_final: -0.0465 (mmt) REVERT: B 88 PHE cc_start: 0.7407 (m-80) cc_final: 0.7026 (m-10) REVERT: B 200 GLN cc_start: 0.7412 (tt0) cc_final: 0.6394 (mm-40) REVERT: B 215 ILE cc_start: 0.7893 (mt) cc_final: 0.7581 (mt) REVERT: B 457 LYS cc_start: 0.7597 (mttm) cc_final: 0.7316 (mttm) REVERT: B 553 HIS cc_start: 0.4858 (t70) cc_final: 0.4436 (t70) REVERT: B 611 MET cc_start: 0.7115 (tpp) cc_final: 0.6678 (tpp) REVERT: B 658 MET cc_start: 0.7832 (ptm) cc_final: 0.7345 (ttp) REVERT: B 757 MET cc_start: 0.0402 (ttp) cc_final: -0.0100 (mmt) outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.2025 time to fit residues: 39.6334 Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 617 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 ASN B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.182872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138275 restraints weight = 30449.546| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.67 r_work: 0.3613 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8974 Z= 0.180 Angle : 0.570 17.674 12182 Z= 0.308 Chirality : 0.038 0.143 1384 Planarity : 0.005 0.053 1472 Dihedral : 4.048 15.652 1190 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 1.10 % Allowed : 8.11 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1084 helix: 1.23 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.53 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 802 TYR 0.016 0.001 TYR B 211 PHE 0.012 0.001 PHE A 423 TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 8972) covalent geometry : angle 0.56968 / 0.31 (12178) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 1.47255 / 0.92 ( 4) hydrogen bonds : bond 0.04987 / 3.32 ( 608) hydrogen bonds : angle 4.98339 / 3.63 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7077 (ttt180) cc_final: 0.6807 (ttm170) REVERT: A 123 TYR cc_start: 0.6767 (t80) cc_final: 0.6287 (t80) REVERT: A 168 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7431 (p0) REVERT: A 215 ILE cc_start: 0.7765 (mt) cc_final: 0.7555 (mt) REVERT: A 300 PHE cc_start: 0.6063 (m-80) cc_final: 0.5656 (m-80) REVERT: A 357 LEU cc_start: 0.7309 (mt) cc_final: 0.6949 (mt) REVERT: A 658 MET cc_start: 0.7789 (ptm) cc_final: 0.6946 (ttp) REVERT: A 757 MET cc_start: -0.0042 (ptt) cc_final: -0.0620 (mmt) REVERT: B 88 PHE cc_start: 0.7317 (m-80) cc_final: 0.6959 (m-10) REVERT: B 92 ASP cc_start: 0.5720 (t70) cc_final: 0.5441 (m-30) REVERT: B 215 ILE cc_start: 0.7780 (mt) cc_final: 0.7559 (mt) REVERT: B 457 LYS cc_start: 0.7432 (mttm) cc_final: 0.7183 (mttm) REVERT: B 611 MET cc_start: 0.6926 (tpp) cc_final: 0.6500 (tpp) REVERT: B 617 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8630 (p) REVERT: B 658 MET cc_start: 0.8038 (ptm) cc_final: 0.7722 (ptt) REVERT: B 757 MET cc_start: 0.0106 (ttp) cc_final: -0.0457 (tpt) outliers start: 10 outliers final: 4 residues processed: 145 average time/residue: 0.2082 time to fit residues: 41.0144 Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141220 restraints weight = 30250.805| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.66 r_work: 0.3648 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8974 Z= 0.126 Angle : 0.536 17.689 12182 Z= 0.285 Chirality : 0.036 0.135 1384 Planarity : 0.005 0.052 1472 Dihedral : 3.923 15.172 1190 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 0.99 % Allowed : 10.42 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1084 helix: 1.49 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.40 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 802 TYR 0.012 0.001 TYR B 211 PHE 0.007 0.001 PHE B 388 TRP 0.010 0.001 TRP A 152 HIS 0.001 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8972) covalent geometry : angle 0.53617 / 0.29 (12178) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 0.98699 / 0.61 ( 4) hydrogen bonds : bond 0.04526 / 3.02 ( 608) hydrogen bonds : angle 4.75439 / 3.48 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7031 (ttt180) cc_final: 0.6761 (ttm170) REVERT: A 168 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7285 (p0) REVERT: A 300 PHE cc_start: 0.5888 (m-80) cc_final: 0.5552 (m-80) REVERT: A 357 LEU cc_start: 0.7208 (mt) cc_final: 0.6852 (mt) REVERT: A 635 ARG cc_start: 0.7652 (mmp80) cc_final: 0.7325 (ttm-80) REVERT: A 757 MET cc_start: -0.0081 (ptt) cc_final: -0.0569 (mmp) REVERT: A 782 GLN cc_start: 0.7630 (pm20) cc_final: 0.7387 (pt0) REVERT: B 88 PHE cc_start: 0.7284 (m-80) cc_final: 0.6975 (m-10) REVERT: B 215 ILE cc_start: 0.7716 (mt) cc_final: 0.7514 (mt) REVERT: B 457 LYS cc_start: 0.7296 (mttm) cc_final: 0.7053 (mttm) REVERT: B 611 MET cc_start: 0.6755 (tpp) cc_final: 0.6348 (tpp) REVERT: B 617 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 757 MET cc_start: 0.0064 (ttp) cc_final: -0.0514 (tpp) outliers start: 9 outliers final: 5 residues processed: 143 average time/residue: 0.1960 time to fit residues: 39.0849 Evaluate side-chains 137 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134616 restraints weight = 30367.484| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.62 r_work: 0.3566 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8974 Z= 0.238 Angle : 0.604 17.517 12182 Z= 0.330 Chirality : 0.039 0.146 1384 Planarity : 0.005 0.057 1472 Dihedral : 4.120 15.298 1190 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.54 % Allowed : 11.40 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1084 helix: 1.19 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.015 0.001 TYR B 211 PHE 0.015 0.001 PHE A 423 TRP 0.011 0.001 TRP B 152 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 ( 8972) covalent geometry : angle 0.60360 / 0.33 (12178) SS BOND : bond 0.00459 / 0.23 ( 2) SS BOND : angle 1.56079 / 0.97 ( 4) hydrogen bonds : bond 0.05119 / 3.40 ( 608) hydrogen bonds : angle 4.98654 / 3.65 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.6840 (t80) cc_final: 0.6268 (t80) REVERT: A 168 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7134 (p0) REVERT: A 635 ARG cc_start: 0.7750 (mmp80) cc_final: 0.7314 (ttp-110) REVERT: A 757 MET cc_start: -0.0309 (ptt) cc_final: -0.0798 (mmt) REVERT: A 782 GLN cc_start: 0.7703 (pm20) cc_final: 0.7269 (pm20) REVERT: B 395 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6833 (mp) REVERT: B 457 LYS cc_start: 0.7373 (mttm) cc_final: 0.7129 (mttm) REVERT: B 611 MET cc_start: 0.6926 (tpp) cc_final: 0.6538 (tpp) REVERT: B 617 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 757 MET cc_start: 0.0404 (ttp) cc_final: -0.0364 (tpt) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.2125 time to fit residues: 41.4783 Evaluate side-chains 140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144261 restraints weight = 29227.681| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.15 r_work: 0.3611 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8974 Z= 0.144 Angle : 0.538 17.672 12182 Z= 0.290 Chirality : 0.037 0.133 1384 Planarity : 0.005 0.062 1472 Dihedral : 3.938 14.796 1190 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.54 % Allowed : 12.28 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1084 helix: 1.43 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.38 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 101 TYR 0.012 0.001 TYR B 211 PHE 0.009 0.001 PHE B 388 TRP 0.013 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8972) covalent geometry : angle 0.53815 / 0.29 (12178) SS BOND : bond 0.00109 / 0.05 ( 2) SS BOND : angle 1.09728 / 0.67 ( 4) hydrogen bonds : bond 0.04593 / 3.04 ( 608) hydrogen bonds : angle 4.75195 / 3.48 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7988 (m-10) cc_final: 0.7704 (m-10) REVERT: A 168 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7324 (p0) REVERT: A 635 ARG cc_start: 0.7814 (mmp80) cc_final: 0.7379 (ttm-80) REVERT: A 757 MET cc_start: -0.0234 (ptt) cc_final: -0.0716 (mmp) REVERT: B 395 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6987 (mp) REVERT: B 457 LYS cc_start: 0.7487 (mttm) cc_final: 0.7260 (mttm) REVERT: B 611 MET cc_start: 0.6988 (tpp) cc_final: 0.6658 (tpp) REVERT: B 617 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 757 MET cc_start: 0.0316 (ttp) cc_final: -0.0404 (tpt) REVERT: B 769 GLU cc_start: 0.6507 (pm20) cc_final: 0.5877 (mm-30) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.1982 time to fit residues: 38.2238 Evaluate side-chains 138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 658 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.184785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141334 restraints weight = 30016.285| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.64 r_work: 0.3639 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8974 Z= 0.114 Angle : 0.516 17.855 12182 Z= 0.276 Chirality : 0.036 0.131 1384 Planarity : 0.005 0.062 1472 Dihedral : 3.759 14.354 1190 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.32 % Allowed : 12.83 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1084 helix: 1.73 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.26 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 101 TYR 0.014 0.001 TYR B 550 PHE 0.010 0.001 PHE B 335 TRP 0.012 0.001 TRP A 152 HIS 0.001 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8972) covalent geometry : angle 0.51589 / 0.28 (12178) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.87779 / 0.53 ( 4) hydrogen bonds : bond 0.04324 / 2.87 ( 608) hydrogen bonds : angle 4.54975 / 3.34 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7887 (m-10) cc_final: 0.7609 (m-10) REVERT: A 95 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6837 (ttm170) REVERT: A 168 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7172 (p0) REVERT: A 195 GLU cc_start: 0.7306 (pm20) cc_final: 0.7001 (pm20) REVERT: A 300 PHE cc_start: 0.5781 (m-80) cc_final: 0.5471 (m-80) REVERT: A 350 TRP cc_start: 0.7361 (m100) cc_final: 0.7119 (m100) REVERT: A 357 LEU cc_start: 0.7233 (mt) cc_final: 0.6877 (mt) REVERT: A 635 ARG cc_start: 0.7777 (mmp80) cc_final: 0.7244 (ttm-80) REVERT: A 757 MET cc_start: -0.0314 (ptt) cc_final: -0.0746 (mmp) REVERT: A 773 ASP cc_start: 0.6510 (m-30) cc_final: 0.6227 (m-30) REVERT: B 457 LYS cc_start: 0.7258 (mttm) cc_final: 0.7011 (mttm) REVERT: B 611 MET cc_start: 0.6754 (tpp) cc_final: 0.6444 (tpp) REVERT: B 617 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 757 MET cc_start: 0.0171 (ttp) cc_final: -0.0812 (tpp) REVERT: B 769 GLU cc_start: 0.6374 (pm20) cc_final: 0.5851 (mm-30) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.2251 time to fit residues: 43.4388 Evaluate side-chains 133 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 658 MET Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137788 restraints weight = 29494.827| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.68 r_work: 0.3545 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8974 Z= 0.168 Angle : 0.543 17.769 12182 Z= 0.293 Chirality : 0.037 0.133 1384 Planarity : 0.005 0.055 1472 Dihedral : 3.822 14.892 1190 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.32 % Allowed : 13.05 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.26), residues: 1084 helix: 1.63 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.27 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.012 0.001 TYR B 211 PHE 0.010 0.001 PHE B 335 TRP 0.010 0.001 TRP A 152 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8972) covalent geometry : angle 0.54251 / 0.29 (12178) SS BOND : bond 0.00226 / 0.11 ( 2) SS BOND : angle 1.10258 / 0.68 ( 4) hydrogen bonds : bond 0.04604 / 3.05 ( 608) hydrogen bonds : angle 4.64978 / 3.41 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6671 (p0) REVERT: A 195 GLU cc_start: 0.7145 (pm20) cc_final: 0.6833 (pm20) REVERT: A 635 ARG cc_start: 0.7661 (mmp80) cc_final: 0.7072 (ttm-80) REVERT: A 757 MET cc_start: -0.0270 (ptt) cc_final: -0.0867 (mmt) REVERT: B 457 LYS cc_start: 0.6922 (mttm) cc_final: 0.6695 (mttp) REVERT: B 611 MET cc_start: 0.6497 (tpp) cc_final: 0.6158 (tpp) REVERT: B 617 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 757 MET cc_start: 0.0214 (ttp) cc_final: -0.0781 (tpp) REVERT: B 769 GLU cc_start: 0.6279 (pm20) cc_final: 0.5797 (mm-30) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.1949 time to fit residues: 34.8417 Evaluate side-chains 131 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 658 MET Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.183763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143626 restraints weight = 29369.804| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.18 r_work: 0.3580 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8974 Z= 0.199 Angle : 0.567 17.754 12182 Z= 0.308 Chirality : 0.038 0.138 1384 Planarity : 0.005 0.055 1472 Dihedral : 3.934 15.279 1190 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.75 % Allowed : 12.50 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1084 helix: 1.49 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.014 0.001 TYR B 211 PHE 0.012 0.001 PHE B 335 TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 8972) covalent geometry : angle 0.56676 / 0.31 (12178) SS BOND : bond 0.00332 / 0.17 ( 2) SS BOND : angle 1.26751 / 0.78 ( 4) hydrogen bonds : bond 0.04831 / 3.20 ( 608) hydrogen bonds : angle 4.76906 / 3.50 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7945 (m-10) cc_final: 0.7691 (m-10) REVERT: A 168 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7211 (p0) REVERT: A 350 TRP cc_start: 0.7531 (m100) cc_final: 0.7313 (m100) REVERT: A 635 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7325 (ttm-80) REVERT: A 757 MET cc_start: -0.0454 (ptt) cc_final: -0.1064 (mmt) REVERT: B 611 MET cc_start: 0.7054 (tpp) cc_final: 0.6755 (tpp) REVERT: B 617 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 757 MET cc_start: 0.0415 (ttp) cc_final: -0.0741 (tpp) REVERT: B 769 GLU cc_start: 0.6540 (pm20) cc_final: 0.6175 (mm-30) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.1952 time to fit residues: 35.9123 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 636 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.184128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139612 restraints weight = 29378.866| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.67 r_work: 0.3568 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8974 Z= 0.120 Angle : 0.520 17.905 12182 Z= 0.278 Chirality : 0.036 0.127 1384 Planarity : 0.005 0.075 1472 Dihedral : 3.789 14.394 1190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.10 % Allowed : 12.94 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1084 helix: 1.75 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.014 0.001 TYR B 550 PHE 0.011 0.001 PHE B 335 TRP 0.012 0.001 TRP A 152 HIS 0.001 0.000 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8972) covalent geometry : angle 0.51985 / 0.28 (12178) SS BOND : bond 0.00000 / 0.00 ( 2) SS BOND : angle 0.91076 / 0.56 ( 4) hydrogen bonds : bond 0.04413 / 2.92 ( 608) hydrogen bonds : angle 4.58118 / 3.37 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 791 is missing expected H atoms. Skipping. Residue LEU 791 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7682 (m-10) cc_final: 0.7466 (m-10) REVERT: A 168 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6686 (p0) REVERT: A 300 PHE cc_start: 0.5471 (m-80) cc_final: 0.5114 (m-80) REVERT: A 635 ARG cc_start: 0.7660 (mmp80) cc_final: 0.6980 (ttm-80) REVERT: A 757 MET cc_start: -0.0417 (ptt) cc_final: -0.0911 (mmt) REVERT: A 769 GLU cc_start: 0.6493 (pm20) cc_final: 0.5169 (mm-30) REVERT: B 88 PHE cc_start: 0.7594 (m-80) cc_final: 0.7388 (m-80) REVERT: B 617 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8324 (p) REVERT: B 769 GLU cc_start: 0.6511 (pm20) cc_final: 0.6118 (mm-30) REVERT: B 782 GLN cc_start: 0.8139 (pm20) cc_final: 0.7724 (pt0) outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.2142 time to fit residues: 37.7462 Evaluate side-chains 127 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.181096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140938 restraints weight = 29545.834| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.23 r_work: 0.3583 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8974 Z= 0.204 Angle : 0.568 17.877 12182 Z= 0.307 Chirality : 0.038 0.139 1384 Planarity : 0.005 0.055 1472 Dihedral : 3.907 14.895 1190 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.43 % Allowed : 12.83 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1084 helix: 1.53 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.013 0.001 TYR B 211 PHE 0.012 0.001 PHE B 335 TRP 0.015 0.001 TRP A 350 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 8972) covalent geometry : angle 0.56726 / 0.31 (12178) SS BOND : bond 0.00342 / 0.17 ( 2) SS BOND : angle 1.20408 / 0.74 ( 4) hydrogen bonds : bond 0.04781 / 3.17 ( 608) hydrogen bonds : angle 4.72974 / 3.47 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.68 seconds wall clock time: 65 minutes 6.72 seconds (3906.72 seconds total)