Starting phenix.real_space_refine on Sun Aug 24 06:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_36200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_36200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_36200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_36200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jev_36200/08_2025/8jev_36200.map" } 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-2.0-5787/lib/python3.9/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, 3 Unusual residues: {' CL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3.60, per 1000 atoms: 0.20 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: 1.64 Conformation dependent library (CDL) restraints added in 693.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 4.54 Time building geometry restraints manager: 2.33 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: 0.03 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: 1.440 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.600 Find NCS groups from input model: 0.270 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 aren 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 covalent geometry : bond 0.00696 ( 8972) covalent geometry : angle 0.73268 (12178) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.35901 ( 4) hydrogen bonds : bond 0.14677 ( 608) hydrogen bonds : angle 7.06584 ( 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 : 0.468 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: 0.2823 time to fit residues: 68.9859 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 : 0.468 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.187961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145421 restraints weight = 30362.705| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.53 r_work: 0.3755 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8974 Z= 0.166 Angle : 0.600 17.496 12182 Z= 0.323 Chirality : 0.038 0.147 1384 Planarity : 0.005 0.053 1472 Dihedral : 4.217 16.293 1190 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 0.88 % Allowed : 5.15 % Favored : 93.97 % 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 aren not related in a simple way. whole: 0.29 (0.25), residues: 1084 helix: 0.99 (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 0.012 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 covalent geometry : bond 0.00361 ( 8972) covalent geometry : angle 0.59923 (12178) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.48052 ( 4) hydrogen bonds : bond 0.05206 ( 608) hydrogen bonds : angle 5.17865 ( 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 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.469 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: 0.6618 (t80) cc_final: 0.6192 (t80) REVERT: A 168 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7709 (p0) REVERT: A 215 ILE cc_start: 0.7858 (mt) cc_final: 0.7548 (mt) REVERT: A 357 LEU cc_start: 0.7538 (mt) cc_final: 0.7183 (mt) REVERT: A 611 MET cc_start: 0.7252 (tpt) cc_final: 0.6828 (tpp) REVERT: A 635 ARG cc_start: 0.7867 (mmp80) cc_final: 0.7482 (ttm110) REVERT: A 658 MET cc_start: 0.7549 (ptm) cc_final: 0.7128 (ttp) REVERT: A 757 MET cc_start: -0.0044 (ptt) cc_final: -0.0461 (mmt) REVERT: B 88 PHE cc_start: 0.7408 (m-80) cc_final: 0.7025 (m-10) REVERT: B 200 GLN cc_start: 0.7417 (tt0) cc_final: 0.6404 (mm-40) REVERT: B 215 ILE cc_start: 0.7889 (mt) cc_final: 0.7576 (mt) REVERT: B 457 LYS cc_start: 0.7592 (mttm) cc_final: 0.7306 (mttm) REVERT: B 553 HIS cc_start: 0.4868 (t70) cc_final: 0.4522 (t-90) REVERT: B 611 MET cc_start: 0.7116 (tpp) cc_final: 0.6678 (tpp) REVERT: B 658 MET cc_start: 0.7834 (ptm) cc_final: 0.7366 (ttp) REVERT: B 757 MET cc_start: 0.0408 (ttp) cc_final: -0.0109 (mmt) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.2558 time to fit residues: 49.1901 Evaluate side-chains 136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 0.5980 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4310 r_free = 0.4310 target = 0.185428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142859 restraints weight = 30695.345| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.54 r_work: 0.3723 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8974 Z= 0.159 Angle : 0.557 17.723 12182 Z= 0.300 Chirality : 0.037 0.140 1384 Planarity : 0.005 0.051 1472 Dihedral : 3.983 15.202 1190 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 1.10 % Allowed : 7.57 % Favored : 91.34 % 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 aren not related in a simple way. whole: 0.72 (0.26), residues: 1084 helix: 1.32 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.016 0.001 TYR B 211 PHE 0.011 0.001 PHE A 423 TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8972) covalent geometry : angle 0.55661 (12178) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.33177 ( 4) hydrogen bonds : bond 0.04867 ( 608) hydrogen bonds : angle 4.92065 ( 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 150 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.487 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: 0.6769 (t80) cc_final: 0.6287 (t80) REVERT: A 168 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7578 (p0) REVERT: A 215 ILE cc_start: 0.8005 (mt) cc_final: 0.7774 (mt) REVERT: A 300 PHE cc_start: 0.6213 (m-80) cc_final: 0.5865 (m-80) REVERT: A 357 LEU cc_start: 0.7665 (mt) cc_final: 0.7336 (mt) REVERT: A 635 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7540 (ttm-80) REVERT: A 658 MET cc_start: 0.7832 (ptm) cc_final: 0.7110 (ttp) REVERT: A 757 MET cc_start: -0.0010 (ptt) cc_final: -0.0576 (mmt) REVERT: B 88 PHE cc_start: 0.7381 (m-80) cc_final: 0.7038 (m-10) REVERT: B 92 ASP cc_start: 0.5981 (t70) cc_final: 0.5613 (m-30) REVERT: B 215 ILE cc_start: 0.8012 (mt) cc_final: 0.7772 (mt) REVERT: B 457 LYS cc_start: 0.7650 (mttm) cc_final: 0.7398 (mttm) REVERT: B 611 MET cc_start: 0.7100 (tpp) cc_final: 0.6700 (tpp) REVERT: B 617 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8584 (p) REVERT: B 658 MET cc_start: 0.8053 (ptm) cc_final: 0.7757 (ptt) REVERT: B 757 MET cc_start: 0.0162 (ttp) cc_final: -0.0340 (tpt) REVERT: B 769 GLU cc_start: 0.6301 (pm20) cc_final: 0.6076 (pm20) outliers start: 10 outliers final: 4 residues processed: 148 average time/residue: 0.2532 time to fit residues: 50.6217 Evaluate side-chains 140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 15 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 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 = 0.4257 r_free = 0.4257 target = 0.185804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141414 restraints weight = 30221.219| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.69 r_work: 0.3649 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8974 Z= 0.129 Angle : 0.536 17.646 12182 Z= 0.285 Chirality : 0.036 0.134 1384 Planarity : 0.005 0.052 1472 Dihedral : 3.907 15.064 1190 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 0.88 % Allowed : 10.09 % Favored : 89.04 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1084 helix: 1.57 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.013 0.001 TYR B 211 PHE 0.008 0.001 PHE B 423 TRP 0.010 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8972) covalent geometry : angle 0.53568 (12178) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.99718 ( 4) hydrogen bonds : bond 0.04524 ( 608) hydrogen bonds : angle 4.73869 ( 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 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.328 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 168 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 300 PHE cc_start: 0.5941 (m-80) cc_final: 0.5632 (m-80) REVERT: A 357 LEU cc_start: 0.7244 (mt) cc_final: 0.6903 (mt) REVERT: A 635 ARG cc_start: 0.7652 (mmp80) cc_final: 0.7350 (ttm-80) REVERT: A 757 MET cc_start: -0.0126 (ptt) cc_final: -0.0579 (mmp) REVERT: A 782 GLN cc_start: 0.7699 (pm20) cc_final: 0.7431 (pt0) REVERT: B 88 PHE cc_start: 0.7305 (m-80) cc_final: 0.6963 (m-10) REVERT: B 92 ASP cc_start: 0.5807 (t70) cc_final: 0.5570 (m-30) REVERT: B 215 ILE cc_start: 0.7753 (mt) cc_final: 0.7549 (mt) REVERT: B 457 LYS cc_start: 0.7312 (mttm) cc_final: 0.7067 (mttm) REVERT: B 611 MET cc_start: 0.6772 (tpp) cc_final: 0.6359 (tpp) REVERT: B 617 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (p) REVERT: B 757 MET cc_start: 0.0067 (ttp) cc_final: -0.0512 (tpp) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.2448 time to fit residues: 48.2432 Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN 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: 0.8980 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4200 r_free = 0.4200 target = 0.179818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135693 restraints weight = 30293.308| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.62 r_work: 0.3564 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8974 Z= 0.236 Angle : 0.599 17.604 12182 Z= 0.326 Chirality : 0.039 0.145 1384 Planarity : 0.005 0.056 1472 Dihedral : 4.062 15.059 1190 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.21 % Allowed : 11.51 % Favored : 87.28 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1084 helix: 1.27 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.015 0.001 TYR B 211 PHE 0.011 0.001 PHE B 423 TRP 0.011 0.001 TRP B 152 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8972) covalent geometry : angle 0.59829 (12178) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.45260 ( 4) hydrogen bonds : bond 0.05039 ( 608) hydrogen bonds : angle 4.94723 ( 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 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.470 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: 0.6815 (t80) cc_final: 0.6219 (t80) REVERT: A 168 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7213 (p0) REVERT: A 635 ARG cc_start: 0.7732 (mmp80) cc_final: 0.7317 (ttp-110) REVERT: A 757 MET cc_start: -0.0196 (ptt) cc_final: -0.0687 (mmt) REVERT: B 457 LYS cc_start: 0.7368 (mttm) cc_final: 0.7119 (mttm) REVERT: B 611 MET cc_start: 0.6909 (tpp) cc_final: 0.6515 (tpp) REVERT: B 617 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 757 MET cc_start: 0.0380 (ttp) cc_final: -0.0361 (tpt) outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.2597 time to fit residues: 49.9736 Evaluate side-chains 141 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 B residue 130 LEU Chi-restraints excluded: chain B residue 224 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: 0.4980 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 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 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 = 0.4122 r_free = 0.4122 target = 0.181894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142397 restraints weight = 29369.269| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.13 r_work: 0.3590 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8974 Z= 0.187 Angle : 0.564 17.592 12182 Z= 0.305 Chirality : 0.037 0.139 1384 Planarity : 0.005 0.061 1472 Dihedral : 4.018 15.307 1190 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.10 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 aren not related in a simple way. whole: 0.73 (0.26), residues: 1084 helix: 1.33 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 101 TYR 0.013 0.001 TYR B 211 PHE 0.009 0.001 PHE B 388 TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8972) covalent geometry : angle 0.56371 (12178) SS BOND : bond 0.00277 ( 2) SS BOND : angle 1.30959 ( 4) hydrogen bonds : bond 0.04802 ( 608) hydrogen bonds : angle 4.85655 ( 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 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.469 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: 0.7985 (m-10) cc_final: 0.7759 (m-10) REVERT: A 123 TYR cc_start: 0.6837 (t80) cc_final: 0.6223 (t80) REVERT: A 168 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7248 (p0) REVERT: A 635 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7401 (ttm-80) REVERT: A 757 MET cc_start: -0.0306 (ptt) cc_final: -0.0810 (mmt) REVERT: A 782 GLN cc_start: 0.7768 (pm20) cc_final: 0.7495 (pt0) REVERT: B 395 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7026 (mp) REVERT: B 457 LYS cc_start: 0.7512 (mttm) cc_final: 0.7283 (mttm) REVERT: B 611 MET cc_start: 0.7083 (tpp) cc_final: 0.6751 (tpp) REVERT: B 617 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 757 MET cc_start: 0.0406 (ttp) cc_final: -0.0405 (tpt) REVERT: B 769 GLU cc_start: 0.6530 (pm20) cc_final: 0.6277 (pm20) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.2688 time to fit residues: 50.8034 Evaluate side-chains 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU 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 528 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 395 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 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 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 = 0.4242 r_free = 0.4242 target = 0.184382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140793 restraints weight = 30027.698| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.65 r_work: 0.3615 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8974 Z= 0.117 Angle : 0.519 17.835 12182 Z= 0.277 Chirality : 0.036 0.128 1384 Planarity : 0.005 0.060 1472 Dihedral : 3.796 14.356 1190 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.64 % Allowed : 12.50 % 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 aren not related in a simple way. whole: 1.23 (0.26), residues: 1084 helix: 1.68 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.30 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 101 TYR 0.012 0.001 TYR B 550 PHE 0.008 0.001 PHE B 388 TRP 0.012 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8972) covalent geometry : angle 0.51905 (12178) SS BOND : bond 0.00010 ( 2) SS BOND : angle 0.95329 ( 4) hydrogen bonds : bond 0.04354 ( 608) hydrogen bonds : angle 4.60532 ( 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 149 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.456 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: 0.7872 (m-10) cc_final: 0.7624 (m-10) REVERT: A 168 ASN cc_start: 0.7366 (OUTLIER) cc_final: 0.7055 (p0) REVERT: A 195 GLU cc_start: 0.7258 (pm20) cc_final: 0.6966 (pm20) REVERT: A 300 PHE cc_start: 0.5831 (m-80) cc_final: 0.5454 (m-80) REVERT: A 357 LEU cc_start: 0.7198 (mt) cc_final: 0.6841 (mt) REVERT: A 635 ARG cc_start: 0.7754 (mmp80) cc_final: 0.7238 (ttm-80) REVERT: A 757 MET cc_start: -0.0299 (ptt) cc_final: -0.0737 (mmp) REVERT: A 782 GLN cc_start: 0.7660 (pm20) cc_final: 0.7434 (pt0) REVERT: B 395 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6814 (mp) REVERT: B 457 LYS cc_start: 0.7254 (mttm) cc_final: 0.7003 (mttp) REVERT: B 611 MET cc_start: 0.6743 (tpp) cc_final: 0.6419 (tpp) REVERT: B 617 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8341 (p) REVERT: B 757 MET cc_start: 0.0020 (ttp) cc_final: -0.0936 (tpp) REVERT: B 769 GLU cc_start: 0.6426 (pm20) cc_final: 0.5866 (mm-30) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.2551 time to fit residues: 49.2237 Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 772 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4164 r_free = 0.4164 target = 0.181840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137226 restraints weight = 29497.871| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.68 r_work: 0.3526 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4336 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= 0.173 Angle : 0.551 17.554 12182 Z= 0.297 Chirality : 0.037 0.136 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.871 15.306 1190 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.21 % Allowed : 13.27 % Favored : 85.53 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1084 helix: 1.60 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 326 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 0.009 0.001 PHE B 388 TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8972) covalent geometry : angle 0.55022 (12178) SS BOND : bond 0.00249 ( 2) SS BOND : angle 1.17147 ( 4) hydrogen bonds : bond 0.04668 ( 608) hydrogen bonds : angle 4.67891 ( 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 138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.427 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 168 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6667 (p0) REVERT: A 195 GLU cc_start: 0.7135 (pm20) cc_final: 0.6830 (pm20) REVERT: A 635 ARG cc_start: 0.7633 (mmp80) cc_final: 0.7106 (ttm-80) REVERT: A 757 MET cc_start: -0.0254 (ptt) cc_final: -0.0863 (mmt) REVERT: A 782 GLN cc_start: 0.7510 (pm20) cc_final: 0.7298 (pt0) REVERT: B 457 LYS cc_start: 0.6910 (mttm) cc_final: 0.6686 (mttp) REVERT: B 611 MET cc_start: 0.6513 (tpp) cc_final: 0.6174 (tpp) REVERT: B 617 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8403 (p) REVERT: B 757 MET cc_start: 0.0200 (ttp) cc_final: -0.0790 (tpp) outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 0.2345 time to fit residues: 42.9381 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 772 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 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: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4112 r_free = 0.4112 target = 0.180873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140468 restraints weight = 29451.098| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.23 r_work: 0.3571 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8974 Z= 0.206 Angle : 0.578 17.625 12182 Z= 0.314 Chirality : 0.038 0.140 1384 Planarity : 0.005 0.055 1472 Dihedral : 4.001 15.609 1190 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.75 % Allowed : 12.83 % Favored : 85.42 % 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 aren not related in a simple way. whole: 0.85 (0.26), residues: 1084 helix: 1.42 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.014 0.001 TYR B 211 PHE 0.010 0.001 PHE B 388 TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8972) covalent geometry : angle 0.57745 (12178) SS BOND : bond 0.00349 ( 2) SS BOND : angle 1.33083 ( 4) hydrogen bonds : bond 0.04903 ( 608) hydrogen bonds : angle 4.80787 ( 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 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.491 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: 0.7894 (m-10) cc_final: 0.7643 (m-10) REVERT: A 168 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7135 (p0) REVERT: A 615 MET cc_start: 0.7583 (mmm) cc_final: 0.7301 (mmt) REVERT: A 635 ARG cc_start: 0.7863 (mmp80) cc_final: 0.7310 (ttm-80) REVERT: A 757 MET cc_start: -0.0538 (ptt) cc_final: -0.1124 (mmt) REVERT: A 782 GLN cc_start: 0.7735 (pm20) cc_final: 0.7498 (pt0) REVERT: B 395 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6941 (mp) REVERT: B 611 MET cc_start: 0.6981 (tpp) cc_final: 0.6676 (tpp) REVERT: B 617 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 757 MET cc_start: 0.0407 (ttp) cc_final: -0.0742 (tpp) REVERT: B 769 GLU cc_start: 0.6782 (pm20) cc_final: 0.6240 (mm-30) outliers start: 16 outliers final: 9 residues processed: 138 average time/residue: 0.2378 time to fit residues: 45.0533 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 : 0.454 ------------------------------------------------------------------------------- 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 636 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 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: 0.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4126 r_free = 0.4126 target = 0.182356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142967 restraints weight = 29359.687| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.14 r_work: 0.3600 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4543 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= 0.158 Angle : 0.549 17.634 12182 Z= 0.294 Chirality : 0.037 0.134 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.917 14.917 1190 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.32 % Allowed : 13.27 % Favored : 85.42 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1084 helix: 1.53 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.36 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.013 0.001 TYR B 550 PHE 0.009 0.001 PHE B 388 TRP 0.012 0.001 TRP A 152 HIS 0.003 0.000 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8972) covalent geometry : angle 0.54820 (12178) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.14886 ( 4) hydrogen bonds : bond 0.04652 ( 608) hydrogen bonds : angle 4.71373 ( 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 136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.409 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: 0.7929 (m-10) cc_final: 0.7663 (m-10) REVERT: A 168 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7141 (p0) REVERT: A 300 PHE cc_start: 0.5921 (m-80) cc_final: 0.5506 (m-80) REVERT: A 635 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7261 (ttm-80) REVERT: A 757 MET cc_start: -0.0511 (ptt) cc_final: -0.1088 (mmt) REVERT: A 782 GLN cc_start: 0.7721 (pm20) cc_final: 0.7504 (pt0) REVERT: B 395 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6964 (mp) REVERT: B 611 MET cc_start: 0.7007 (tpp) cc_final: 0.6734 (tpp) REVERT: B 617 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8472 (p) REVERT: B 769 GLU cc_start: 0.6821 (pm20) cc_final: 0.6228 (mm-30) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.2445 time to fit residues: 44.6395 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 : 0.458 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 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 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 = 0.4182 r_free = 0.4182 target = 0.183690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139298 restraints weight = 29430.441| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.67 r_work: 0.3575 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8974 Z= 0.130 Angle : 0.530 17.890 12182 Z= 0.283 Chirality : 0.037 0.128 1384 Planarity : 0.004 0.053 1472 Dihedral : 3.780 14.323 1190 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.21 % Allowed : 13.16 % 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 aren not related in a simple way. whole: 1.28 (0.26), residues: 1084 helix: 1.70 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.25 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.014 0.001 TYR B 550 PHE 0.009 0.001 PHE B 388 TRP 0.012 0.001 TRP B 350 HIS 0.002 0.000 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8972) covalent geometry : angle 0.53027 (12178) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.95267 ( 4) hydrogen bonds : bond 0.04446 ( 608) hydrogen bonds : angle 4.59224 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.83 seconds wall clock time: 76 minutes 0.60 seconds (4560.60 seconds total)