Starting phenix.real_space_refine on Mon Nov 18 21:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_36200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_36200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_36200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_36200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jev_36200/11_2024/8jev_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-5513/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: 9.13, per 1000 atoms: 0.52 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: 4.78 Conformation dependent library (CDL) restraints added in 1.7 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: 1.41 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: 7.14 Time building geometry restraints manager: 5.72 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: 0.00 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: 1.140 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: 0.320 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 41.090 Find NCS groups from input model: 0.430 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.850 ------------------------------------------------------------------------------- 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 8972 Z= 0.432 Angle : 0.733 17.619 12178 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 *********************** 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 : 1.436 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: 0.5825 time to fit residues: 144.3227 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 : 1.318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 8972 Z= 0.189 Angle : 0.590 17.553 12178 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 *********************** 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 : 1.482 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: 0.6885 (t80) cc_final: 0.6334 (t80) REVERT: A 215 ILE cc_start: 0.7832 (mt) cc_final: 0.7554 (mt) REVERT: A 658 MET cc_start: 0.7306 (ptm) cc_final: 0.6799 (ttp) REVERT: A 757 MET cc_start: 0.0217 (ptt) cc_final: -0.0280 (mmt) REVERT: B 200 GLN cc_start: 0.7198 (tt0) cc_final: 0.6762 (mm-40) REVERT: B 215 ILE cc_start: 0.7889 (mt) cc_final: 0.7583 (mt) REVERT: B 457 LYS cc_start: 0.7848 (mttm) cc_final: 0.7539 (mttm) REVERT: B 611 MET cc_start: 0.6705 (tpp) cc_final: 0.6474 (tpp) REVERT: B 658 MET cc_start: 0.7467 (ptm) cc_final: 0.6899 (ttp) REVERT: B 757 MET cc_start: 0.0488 (ttp) cc_final: -0.0001 (mmt) outliers start: 8 outliers final: 4 residues processed: 146 average time/residue: 0.5221 time to fit residues: 103.1162 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 55 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8972 Z= 0.223 Angle : 0.569 17.813 12178 Z= 0.305 Chirality : 0.037 0.140 1384 Planarity : 0.005 0.053 1472 Dihedral : 3.997 16.009 1190 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 1.10 % Allowed : 8.22 % 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: 0.73 (0.26), residues: 1084 helix: 1.29 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.44 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS B 552 PHE 0.013 0.001 PHE B 423 TYR 0.016 0.001 TYR B 211 ARG 0.004 0.000 ARG B 802 *********************** 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 143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.7038 (t80) cc_final: 0.6414 (t80) REVERT: A 215 ILE cc_start: 0.7977 (mt) cc_final: 0.7738 (mt) REVERT: A 658 MET cc_start: 0.7469 (ptm) cc_final: 0.6518 (ttp) REVERT: A 757 MET cc_start: 0.0197 (ptt) cc_final: -0.0379 (mmt) REVERT: B 88 PHE cc_start: 0.8106 (m-10) cc_final: 0.7730 (m-80) REVERT: B 215 ILE cc_start: 0.8027 (mt) cc_final: 0.7763 (mt) REVERT: B 457 LYS cc_start: 0.7889 (mttm) cc_final: 0.7633 (mttp) REVERT: B 611 MET cc_start: 0.6745 (tpp) cc_final: 0.6540 (tpp) REVERT: B 617 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 658 MET cc_start: 0.7642 (ptm) cc_final: 0.6849 (ptt) REVERT: B 757 MET cc_start: 0.0343 (ttp) cc_final: -0.0213 (tpt) outliers start: 10 outliers final: 4 residues processed: 141 average time/residue: 0.4897 time to fit residues: 95.9913 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 : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8972 Z= 0.228 Angle : 0.554 17.607 12178 Z= 0.297 Chirality : 0.037 0.136 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.988 15.668 1190 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.27 % 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: 0.87 (0.26), residues: 1084 helix: 1.39 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.002 0.001 HIS B 552 PHE 0.009 0.001 PHE A 423 TYR 0.014 0.001 TYR B 211 ARG 0.006 0.000 ARG B 802 *********************** 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 150 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.351 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 123 TYR cc_start: 0.7130 (t80) cc_final: 0.6422 (t80) REVERT: A 757 MET cc_start: -0.0049 (ptt) cc_final: -0.0582 (mmt) REVERT: B 88 PHE cc_start: 0.8215 (m-10) cc_final: 0.7906 (m-80) REVERT: B 215 ILE cc_start: 0.8087 (mt) cc_final: 0.7869 (mt) REVERT: B 457 LYS cc_start: 0.7882 (mttm) cc_final: 0.7505 (mttm) REVERT: B 617 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 658 MET cc_start: 0.7671 (ptm) cc_final: 0.7326 (ptt) REVERT: B 757 MET cc_start: 0.0437 (ttp) cc_final: -0.0155 (tpp) outliers start: 8 outliers final: 5 residues processed: 147 average time/residue: 0.5267 time to fit residues: 104.5943 Evaluate side-chains 136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8972 Z= 0.223 Angle : 0.551 17.700 12178 Z= 0.295 Chirality : 0.037 0.135 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.924 14.654 1190 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.10 % Allowed : 11.84 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.26), residues: 1084 helix: 1.46 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.33 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.003 0.001 HIS B 633 PHE 0.009 0.001 PHE A 423 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.000 ARG B 802 *********************** 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 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.300 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 123 TYR cc_start: 0.7112 (t80) cc_final: 0.6382 (t80) REVERT: A 757 MET cc_start: -0.0171 (ptt) cc_final: -0.0707 (mmp) REVERT: A 782 GLN cc_start: 0.8087 (pm20) cc_final: 0.7797 (pt0) REVERT: B 88 PHE cc_start: 0.8231 (m-10) cc_final: 0.7931 (m-80) REVERT: B 395 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7229 (mp) REVERT: B 457 LYS cc_start: 0.7950 (mttm) cc_final: 0.7671 (mttp) REVERT: B 617 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7985 (p) REVERT: B 658 MET cc_start: 0.7672 (ptm) cc_final: 0.7187 (ptt) REVERT: B 757 MET cc_start: 0.0444 (ttp) cc_final: -0.0268 (tpt) outliers start: 10 outliers final: 7 residues processed: 140 average time/residue: 0.5067 time to fit residues: 97.2386 Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8972 Z= 0.185 Angle : 0.532 17.687 12178 Z= 0.284 Chirality : 0.037 0.131 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.835 14.332 1190 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.10 % Allowed : 11.95 % Favored : 86.95 % 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: 1.17 (0.26), residues: 1084 helix: 1.61 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.000 HIS B 633 PHE 0.008 0.001 PHE B 388 TYR 0.012 0.001 TYR B 211 ARG 0.007 0.000 ARG B 101 *********************** 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 140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.404 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 757 MET cc_start: -0.0043 (ptt) cc_final: -0.0638 (mmp) REVERT: A 782 GLN cc_start: 0.8171 (pm20) cc_final: 0.7907 (pt0) REVERT: B 395 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7232 (mp) REVERT: B 457 LYS cc_start: 0.7894 (mttm) cc_final: 0.7614 (mttp) REVERT: B 617 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7955 (p) REVERT: B 757 MET cc_start: 0.0296 (ttp) cc_final: -0.0480 (tpt) outliers start: 10 outliers final: 6 residues processed: 136 average time/residue: 0.5223 time to fit residues: 97.2361 Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8972 Z= 0.195 Angle : 0.535 17.763 12178 Z= 0.287 Chirality : 0.037 0.131 1384 Planarity : 0.005 0.069 1472 Dihedral : 3.817 14.273 1190 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.88 % Allowed : 12.39 % Favored : 86.73 % 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: 1.23 (0.26), residues: 1084 helix: 1.66 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.24 (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 0.011 0.001 PHE B 88 TYR 0.012 0.001 TYR B 211 ARG 0.011 0.000 ARG A 101 *********************** 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 137 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 TRP cc_start: 0.7425 (m100) cc_final: 0.7211 (m100) REVERT: A 757 MET cc_start: -0.0090 (ptt) cc_final: -0.0681 (mmp) REVERT: B 88 PHE cc_start: 0.7999 (m-80) cc_final: 0.7483 (m-80) REVERT: B 457 LYS cc_start: 0.7872 (mttm) cc_final: 0.7645 (mttm) REVERT: B 617 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7904 (p) REVERT: B 757 MET cc_start: 0.0298 (ttp) cc_final: -0.0538 (tpt) REVERT: B 769 GLU cc_start: 0.6566 (pm20) cc_final: 0.6283 (mm-30) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.4937 time to fit residues: 91.1335 Evaluate side-chains 132 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8972 Z= 0.222 Angle : 0.540 17.810 12178 Z= 0.291 Chirality : 0.037 0.134 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.836 15.290 1190 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 1.17 (0.26), residues: 1084 helix: 1.61 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 324 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 0.008 0.001 PHE B 388 TYR 0.012 0.001 TYR B 211 ARG 0.005 0.000 ARG A 101 *********************** 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 : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: -0.0157 (ptt) cc_final: -0.0859 (mmt) REVERT: B 395 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7247 (mp) REVERT: B 457 LYS cc_start: 0.7876 (mttm) cc_final: 0.7649 (mttm) REVERT: B 617 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 757 MET cc_start: 0.0562 (ttp) cc_final: -0.0538 (tpp) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.4933 time to fit residues: 90.8906 Evaluate side-chains 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 772 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 547 GLN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8972 Z= 0.191 Angle : 0.530 17.811 12178 Z= 0.284 Chirality : 0.036 0.129 1384 Planarity : 0.004 0.054 1472 Dihedral : 3.782 14.103 1190 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.77 % Allowed : 13.05 % 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: 1.28 (0.26), residues: 1084 helix: 1.70 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 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 0.003 0.000 ARG B 101 *********************** 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 132 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 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: A 757 MET cc_start: -0.0083 (ptt) cc_final: -0.0768 (mmt) REVERT: B 88 PHE cc_start: 0.8175 (m-80) cc_final: 0.7840 (m-80) REVERT: B 457 LYS cc_start: 0.7869 (mttm) cc_final: 0.7640 (mttm) REVERT: B 617 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 757 MET cc_start: 0.0562 (ttp) cc_final: -0.0544 (tpp) REVERT: B 782 GLN cc_start: 0.8477 (pm20) cc_final: 0.8121 (pt0) outliers start: 7 outliers final: 6 residues processed: 130 average time/residue: 0.4728 time to fit residues: 85.4466 Evaluate side-chains 130 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 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 49 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8972 Z= 0.154 Angle : 0.514 17.849 12178 Z= 0.273 Chirality : 0.036 0.130 1384 Planarity : 0.004 0.053 1472 Dihedral : 3.676 14.311 1190 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.99 % Allowed : 12.61 % 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: 1.40 (0.26), residues: 1084 helix: 1.81 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 312 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 0.008 0.001 PHE B 388 TYR 0.015 0.001 TYR B 550 ARG 0.003 0.000 ARG B 101 ********************** 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 135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.384 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 423 PHE cc_start: 0.6935 (m-10) cc_final: 0.6603 (m-10) REVERT: A 757 MET cc_start: -0.0153 (ptt) cc_final: -0.0796 (mmt) REVERT: B 88 PHE cc_start: 0.8168 (m-80) cc_final: 0.7829 (m-80) REVERT: B 423 PHE cc_start: 0.6915 (m-10) cc_final: 0.6509 (m-10) REVERT: B 457 LYS cc_start: 0.7849 (mttm) cc_final: 0.7632 (mttm) REVERT: B 617 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 782 GLN cc_start: 0.8344 (pm20) cc_final: 0.8072 (pt0) outliers start: 9 outliers final: 8 residues processed: 131 average time/residue: 0.4617 time to fit residues: 85.6821 Evaluate side-chains 128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.183388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138792 restraints weight = 29564.942| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.68 r_work: 0.3578 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8972 Z= 0.216 Angle : 0.537 17.834 12178 Z= 0.287 Chirality : 0.037 0.132 1384 Planarity : 0.005 0.054 1472 Dihedral : 3.739 14.288 1190 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.10 % Allowed : 12.39 % Favored : 86.51 % 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: 1.72 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 350 HIS 0.004 0.001 HIS B 633 PHE 0.008 0.001 PHE B 388 TYR 0.014 0.001 TYR B 550 ARG 0.003 0.000 ARG B 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.93 seconds wall clock time: 75 minutes 6.91 seconds (4506.91 seconds total)