Starting phenix.real_space_refine on Sun May 18 21:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jev_36200/05_2025/8jev_36200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jev_36200/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jev_36200/05_2025/8jev_36200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jev_36200/05_2025/8jev_36200.map" model { file = "/net/cci-nas-00/data/ceres_data/8jev_36200/05_2025/8jev_36200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jev_36200/05_2025/8jev_36200.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.23, per 1000 atoms: 0.47 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: 4.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.19 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: 6.23 Time building geometry restraints manager: 5.43 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: 0.05 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 37.060 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (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 TRP 0.023 0.002 TRP A 93 HIS 0.006 0.001 HIS B 633 PHE 0.012 0.002 PHE A 775 TYR 0.024 0.002 TYR A 211 ARG 0.010 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.14677 ( 608) hydrogen bonds : angle 7.06584 ( 1797) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.35901 ( 4) covalent geometry : bond 0.00696 ( 8972) covalent geometry : angle 0.73268 (12178) *********************** 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 : 1.181 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: 0.7621 (mt) REVERT: A 658 MET cc_start: 0.7335 (ptm) cc_final: 0.7029 (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: 0.6829 (mm-40) REVERT: B 215 ILE cc_start: 0.7907 (mt) cc_final: 0.7580 (mt) REVERT: B 457 LYS cc_start: 0.7862 (mttm) cc_final: 0.7573 (mttm) REVERT: B 658 MET cc_start: 0.7500 (ptm) cc_final: 0.7037 (ttp) REVERT: B 757 MET cc_start: 0.0341 (ttp) cc_final: -0.0132 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.5362 time to fit residues: 132.2264 Evaluate side-chains 125 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147313 restraints weight = 30394.679| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.53 r_work: 0.3777 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8974 Z= 0.143 Angle : 0.591 17.553 12182 Z= 0.316 Chirality : 0.037 0.143 1384 Planarity : 0.005 0.052 1472 Dihedral : 4.215 16.679 1190 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1084 helix: 1.06 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.003 0.001 HIS A 552 PHE 0.012 0.001 PHE B 775 TYR 0.014 0.001 TYR B 211 ARG 0.005 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 608) hydrogen bonds : angle 5.15683 ( 1797) SS BOND : bond 0.00173 ( 2) SS BOND : angle 1.29735 ( 4) covalent geometry : bond 0.00306 ( 8972) covalent geometry : angle 0.59040 (12178) *********************** 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 151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.182 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: 0.7149 (ttt180) cc_final: 0.6939 (ttm170) REVERT: A 123 TYR cc_start: 0.6592 (t80) cc_final: 0.6160 (t80) REVERT: A 168 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7697 (p0) REVERT: A 215 ILE cc_start: 0.7785 (mt) cc_final: 0.7476 (mt) REVERT: A 357 LEU cc_start: 0.7461 (mt) cc_final: 0.7111 (mt) REVERT: A 611 MET cc_start: 0.7190 (tpt) cc_final: 0.6761 (tpp) REVERT: A 635 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7429 (ttm110) REVERT: A 658 MET cc_start: 0.7527 (ptm) cc_final: 0.7115 (ttp) REVERT: A 757 MET cc_start: 0.0059 (ptt) cc_final: -0.0414 (mmt) REVERT: B 88 PHE cc_start: 0.7354 (m-80) cc_final: 0.6981 (m-10) REVERT: B 200 GLN cc_start: 0.7383 (tt0) cc_final: 0.6367 (mm-40) REVERT: B 215 ILE cc_start: 0.7826 (mt) cc_final: 0.7512 (mt) REVERT: B 457 LYS cc_start: 0.7568 (mttm) cc_final: 0.7295 (mttm) REVERT: B 611 MET cc_start: 0.7057 (tpp) cc_final: 0.6602 (tpp) REVERT: B 658 MET cc_start: 0.7816 (ptm) cc_final: 0.7365 (ttp) REVERT: B 757 MET cc_start: 0.0380 (ttp) cc_final: -0.0137 (mmt) outliers start: 8 outliers final: 4 residues processed: 146 average time/residue: 0.4969 time to fit residues: 98.5664 Evaluate side-chains 137 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.186957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144496 restraints weight = 30339.321| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.53 r_work: 0.3746 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8974 Z= 0.145 Angle : 0.547 17.752 12182 Z= 0.294 Chirality : 0.037 0.138 1384 Planarity : 0.005 0.052 1472 Dihedral : 3.961 15.066 1190 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.40 % Rotamer: Outliers : 0.99 % Allowed : 8.33 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1084 helix: 1.42 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.003 0.001 HIS B 553 PHE 0.010 0.001 PHE B 423 TYR 0.015 0.001 TYR B 211 ARG 0.004 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 608) hydrogen bonds : angle 4.87326 ( 1797) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.22736 ( 4) covalent geometry : bond 0.00324 ( 8972) covalent geometry : angle 0.54714 (12178) *********************** 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 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.401 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 123 TYR cc_start: 0.6664 (t80) cc_final: 0.6203 (t80) REVERT: A 168 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7602 (p0) REVERT: A 215 ILE cc_start: 0.7966 (mt) cc_final: 0.7701 (mt) REVERT: A 300 PHE cc_start: 0.6191 (m-80) cc_final: 0.5987 (m-80) REVERT: A 357 LEU cc_start: 0.7668 (mt) cc_final: 0.7357 (mt) REVERT: A 635 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7554 (ttm-80) REVERT: A 658 MET cc_start: 0.7714 (ptm) cc_final: 0.7002 (ttp) REVERT: A 757 MET cc_start: -0.0070 (ptt) cc_final: -0.0505 (mmt) REVERT: B 88 PHE cc_start: 0.7431 (m-80) cc_final: 0.7066 (m-10) REVERT: B 92 ASP cc_start: 0.5925 (t70) cc_final: 0.5597 (m-30) REVERT: B 215 ILE cc_start: 0.8022 (mt) cc_final: 0.7760 (mt) REVERT: B 457 LYS cc_start: 0.7672 (mttm) cc_final: 0.7436 (mttp) REVERT: B 611 MET cc_start: 0.7130 (tpp) cc_final: 0.6715 (tpp) REVERT: B 617 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8582 (p) REVERT: B 757 MET cc_start: 0.0206 (ttp) cc_final: -0.0288 (tpt) REVERT: B 769 GLU cc_start: 0.6356 (pm20) cc_final: 0.6117 (pm20) outliers start: 9 outliers final: 3 residues processed: 140 average time/residue: 0.5128 time to fit residues: 100.6949 Evaluate side-chains 133 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** A 637 ASN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.181652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139391 restraints weight = 29886.746| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.55 r_work: 0.3626 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3550 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= 0.168 Angle : 0.556 17.546 12182 Z= 0.300 Chirality : 0.037 0.139 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.968 17.342 1190 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 1.21 % Allowed : 10.64 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1084 helix: 1.42 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.40 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.002 0.001 HIS B 633 PHE 0.014 0.001 PHE A 423 TYR 0.014 0.001 TYR B 211 ARG 0.005 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 608) hydrogen bonds : angle 4.82080 ( 1797) SS BOND : bond 0.00240 ( 2) SS BOND : angle 1.23380 ( 4) covalent geometry : bond 0.00384 ( 8972) covalent geometry : angle 0.55538 (12178) *********************** 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 154 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.362 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 123 TYR cc_start: 0.6763 (t80) cc_final: 0.6281 (t80) REVERT: A 168 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7414 (p0) REVERT: A 300 PHE cc_start: 0.5992 (m-80) cc_final: 0.5591 (m-80) REVERT: A 635 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7379 (ttm-80) REVERT: A 757 MET cc_start: -0.0238 (ptt) cc_final: -0.0742 (mmt) REVERT: B 215 ILE cc_start: 0.7809 (mt) cc_final: 0.7606 (mt) REVERT: B 457 LYS cc_start: 0.7387 (mttm) cc_final: 0.7072 (mttm) REVERT: B 611 MET cc_start: 0.6835 (tpp) cc_final: 0.6428 (tpp) REVERT: B 617 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 757 MET cc_start: 0.0234 (ttp) cc_final: -0.0386 (tpp) REVERT: B 769 GLU cc_start: 0.6354 (pm20) cc_final: 0.6151 (pm20) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 0.5267 time to fit residues: 106.3365 Evaluate side-chains 141 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.183815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140390 restraints weight = 30634.421| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.63 r_work: 0.3610 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3886 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= 0.141 Angle : 0.537 17.732 12182 Z= 0.287 Chirality : 0.037 0.133 1384 Planarity : 0.005 0.053 1472 Dihedral : 3.855 14.333 1190 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.10 % Allowed : 11.73 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1084 helix: 1.56 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.003 0.000 HIS B 633 PHE 0.009 0.001 PHE A 423 TYR 0.013 0.001 TYR B 211 ARG 0.005 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 608) hydrogen bonds : angle 4.71469 ( 1797) SS BOND : bond 0.00112 ( 2) SS BOND : angle 1.05828 ( 4) covalent geometry : bond 0.00315 ( 8972) covalent geometry : angle 0.53629 (12178) *********************** 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: 10 poor density : 138 time to evaluate : 1.615 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: 0.7406 (OUTLIER) cc_final: 0.7140 (p0) REVERT: A 300 PHE cc_start: 0.5832 (m-80) cc_final: 0.5452 (m-80) REVERT: A 357 LEU cc_start: 0.7145 (mt) cc_final: 0.6782 (mt) REVERT: A 635 ARG cc_start: 0.7785 (mmp80) cc_final: 0.7295 (ttm-80) REVERT: A 757 MET cc_start: -0.0164 (ptt) cc_final: -0.0644 (mmp) REVERT: A 782 GLN cc_start: 0.7635 (pm20) cc_final: 0.7347 (pt0) REVERT: B 395 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6675 (mp) REVERT: B 457 LYS cc_start: 0.7251 (mttm) cc_final: 0.7001 (mttp) REVERT: B 611 MET cc_start: 0.6667 (tpp) cc_final: 0.6279 (tpp) REVERT: B 617 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8403 (p) REVERT: B 757 MET cc_start: 0.0310 (ttp) cc_final: -0.0283 (tpt) outliers start: 10 outliers final: 6 residues processed: 143 average time/residue: 0.5090 time to fit residues: 99.4684 Evaluate side-chains 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.183839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140028 restraints weight = 30283.426| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.66 r_work: 0.3640 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.4065 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= 0.131 Angle : 0.528 17.811 12182 Z= 0.282 Chirality : 0.036 0.131 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.760 14.426 1190 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.32 % Allowed : 11.51 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1084 helix: 1.71 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 PHE 0.013 0.001 PHE B 88 TYR 0.012 0.001 TYR B 211 ARG 0.002 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 608) hydrogen bonds : angle 4.61546 ( 1797) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.98177 ( 4) covalent geometry : bond 0.00291 ( 8972) covalent geometry : angle 0.52787 (12178) *********************** 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 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.178 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 168 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7255 (p0) REVERT: A 195 GLU cc_start: 0.7308 (pm20) cc_final: 0.7051 (pm20) REVERT: A 235 TYR cc_start: 0.8269 (m-80) cc_final: 0.8036 (m-10) REVERT: A 635 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7322 (ttm-80) REVERT: A 757 MET cc_start: -0.0265 (ptt) cc_final: -0.0706 (mmp) REVERT: A 782 GLN cc_start: 0.7742 (pm20) cc_final: 0.7483 (pt0) REVERT: B 457 LYS cc_start: 0.7294 (mttm) cc_final: 0.7046 (mttp) REVERT: B 611 MET cc_start: 0.6764 (tpp) cc_final: 0.6403 (tpp) REVERT: B 617 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 757 MET cc_start: 0.0067 (ttp) cc_final: -0.0614 (tpt) REVERT: B 769 GLU cc_start: 0.6391 (pm20) cc_final: 0.5809 (mm-30) outliers start: 12 outliers final: 8 residues processed: 138 average time/residue: 0.5165 time to fit residues: 96.5977 Evaluate side-chains 138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 421 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.182277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140178 restraints weight = 29994.037| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.57 r_work: 0.3630 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8974 Z= 0.133 Angle : 0.525 17.803 12182 Z= 0.281 Chirality : 0.036 0.131 1384 Planarity : 0.005 0.066 1472 Dihedral : 3.749 14.365 1190 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.10 % Allowed : 12.50 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1084 helix: 1.78 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.20 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.003 0.000 HIS B 633 PHE 0.009 0.001 PHE A 423 TYR 0.012 0.001 TYR B 211 ARG 0.010 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 608) hydrogen bonds : angle 4.56303 ( 1797) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.94680 ( 4) covalent geometry : bond 0.00295 ( 8972) covalent geometry : angle 0.52507 (12178) *********************** 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 141 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.400 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: 0.7440 (OUTLIER) cc_final: 0.7187 (p0) REVERT: A 195 GLU cc_start: 0.7283 (pm20) cc_final: 0.6987 (pm20) REVERT: A 235 TYR cc_start: 0.8279 (m-80) cc_final: 0.8064 (m-10) REVERT: A 635 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7268 (ttm-80) REVERT: A 757 MET cc_start: -0.0267 (ptt) cc_final: -0.0720 (mmp) REVERT: A 782 GLN cc_start: 0.7698 (pm20) cc_final: 0.7470 (pt0) REVERT: B 611 MET cc_start: 0.6772 (tpp) cc_final: 0.6400 (tpp) REVERT: B 617 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8401 (p) REVERT: B 757 MET cc_start: 0.0053 (ttp) cc_final: -0.0652 (tpt) REVERT: B 769 GLU cc_start: 0.6429 (pm20) cc_final: 0.5853 (mm-30) outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 0.5273 time to fit residues: 97.5639 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 421 THR 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 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 70 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.180832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136857 restraints weight = 29446.209| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.63 r_work: 0.3565 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8974 Z= 0.162 Angle : 0.542 17.652 12182 Z= 0.293 Chirality : 0.037 0.135 1384 Planarity : 0.005 0.066 1472 Dihedral : 3.813 14.178 1190 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.21 % Allowed : 12.50 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1084 helix: 1.69 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B 633 PHE 0.011 0.001 PHE A 423 TYR 0.013 0.001 TYR B 211 ARG 0.012 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 608) hydrogen bonds : angle 4.62633 ( 1797) SS BOND : bond 0.00205 ( 2) SS BOND : angle 1.05335 ( 4) covalent geometry : bond 0.00367 ( 8972) covalent geometry : angle 0.54177 (12178) *********************** 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 : 1.322 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: 0.7056 (OUTLIER) cc_final: 0.6674 (p0) REVERT: A 195 GLU cc_start: 0.7092 (pm20) cc_final: 0.6767 (pm20) REVERT: A 235 TYR cc_start: 0.8163 (m-80) cc_final: 0.7933 (m-10) REVERT: A 635 ARG cc_start: 0.7683 (mmp80) cc_final: 0.7019 (ttm-80) REVERT: A 757 MET cc_start: -0.0314 (ptt) cc_final: -0.0882 (mmt) REVERT: A 782 GLN cc_start: 0.7488 (pm20) cc_final: 0.7270 (pt0) REVERT: B 611 MET cc_start: 0.6433 (tpp) cc_final: 0.6085 (tpp) REVERT: B 617 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 757 MET cc_start: 0.0235 (ttp) cc_final: -0.0798 (tpp) REVERT: B 769 GLU cc_start: 0.6277 (pm20) cc_final: 0.5754 (mm-30) REVERT: B 782 GLN cc_start: 0.8172 (pm20) cc_final: 0.7800 (pt0) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.5092 time to fit residues: 92.4592 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 : 1.290 ------------------------------------------------------------------------------- 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 421 THR 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 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 86 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.185369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141332 restraints weight = 29401.089| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.68 r_work: 0.3582 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8974 Z= 0.114 Angle : 0.514 17.898 12182 Z= 0.274 Chirality : 0.036 0.127 1384 Planarity : 0.005 0.068 1472 Dihedral : 3.699 14.253 1190 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.21 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1084 helix: 1.92 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 PHE 0.007 0.001 PHE B 388 TYR 0.013 0.001 TYR B 550 ARG 0.010 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 608) hydrogen bonds : angle 4.48484 ( 1797) SS BOND : bond 0.00018 ( 2) SS BOND : angle 0.84968 ( 4) covalent geometry : bond 0.00244 ( 8972) covalent geometry : angle 0.51365 (12178) *********************** 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 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.257 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: 0.6990 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 195 GLU cc_start: 0.7057 (pm20) cc_final: 0.6731 (pm20) REVERT: A 300 PHE cc_start: 0.5513 (m-80) cc_final: 0.5194 (m-80) REVERT: A 635 ARG cc_start: 0.7650 (mmp80) cc_final: 0.6996 (ttm-80) REVERT: A 757 MET cc_start: -0.0306 (ptt) cc_final: -0.0711 (mmp) REVERT: A 782 GLN cc_start: 0.7719 (pm20) cc_final: 0.7465 (pt0) REVERT: B 423 PHE cc_start: 0.6371 (m-10) cc_final: 0.6111 (m-10) REVERT: B 611 MET cc_start: 0.6418 (tpp) cc_final: 0.6119 (tpp) REVERT: B 617 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (p) REVERT: B 757 MET cc_start: 0.0016 (ttp) cc_final: -0.0906 (tpp) REVERT: B 769 GLU cc_start: 0.6217 (pm20) cc_final: 0.5777 (mm-30) REVERT: B 782 GLN cc_start: 0.8102 (pm20) cc_final: 0.7837 (pt0) outliers start: 11 outliers final: 9 residues processed: 134 average time/residue: 0.4852 time to fit residues: 88.1470 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 421 THR 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 196 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 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 19 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.183890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144052 restraints weight = 29424.138| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.17 r_work: 0.3601 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8974 Z= 0.206 Angle : 0.570 17.735 12182 Z= 0.309 Chirality : 0.038 0.142 1384 Planarity : 0.005 0.056 1472 Dihedral : 3.888 15.424 1190 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.10 % Allowed : 12.83 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1084 helix: 1.61 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.30 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.005 0.001 HIS B 633 PHE 0.010 0.001 PHE A 423 TYR 0.014 0.001 TYR B 211 ARG 0.006 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 608) hydrogen bonds : angle 4.69297 ( 1797) SS BOND : bond 0.00355 ( 2) SS BOND : angle 1.21518 ( 4) covalent geometry : bond 0.00471 ( 8972) covalent geometry : angle 0.56982 (12178) ********************** 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 141 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.204 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: 0.7680 (OUTLIER) cc_final: 0.7284 (p0) REVERT: A 635 ARG cc_start: 0.7895 (mmp80) cc_final: 0.7312 (ttm-80) REVERT: A 757 MET cc_start: -0.0390 (ptt) cc_final: -0.0877 (mmp) REVERT: A 782 GLN cc_start: 0.7960 (pm20) cc_final: 0.7759 (pt0) REVERT: B 611 MET cc_start: 0.7062 (tpp) cc_final: 0.6760 (tpp) REVERT: B 617 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 658 MET cc_start: 0.7873 (ptt) cc_final: 0.7499 (ptp) REVERT: B 757 MET cc_start: 0.0432 (ttp) cc_final: -0.0714 (tpp) REVERT: B 769 GLU cc_start: 0.6462 (pm20) cc_final: 0.5988 (mm-30) REVERT: B 782 GLN cc_start: 0.8415 (pm20) cc_final: 0.8037 (pt0) outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 0.5073 time to fit residues: 93.7424 Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 421 THR 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 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 49 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4138 r_free = 0.4138 target = 0.183774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143817 restraints weight = 29407.584| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.23 r_work: 0.3627 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.4586 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= 0.144 Angle : 0.533 17.963 12182 Z= 0.285 Chirality : 0.036 0.132 1384 Planarity : 0.005 0.055 1472 Dihedral : 3.800 14.506 1190 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1084 helix: 1.74 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.003 0.000 HIS B 633 PHE 0.008 0.001 PHE B 388 TYR 0.013 0.001 TYR B 550 ARG 0.006 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 608) hydrogen bonds : angle 4.58963 ( 1797) SS BOND : bond 0.00129 ( 2) SS BOND : angle 1.03135 ( 4) covalent geometry : bond 0.00321 ( 8972) covalent geometry : angle 0.53259 (12178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8467.33 seconds wall clock time: 145 minutes 52.63 seconds (8752.63 seconds total)