Starting phenix.real_space_refine on Sun Jun 15 16:20:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jev_36200/06_2025/8jev_36200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jev_36200/06_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_36200/06_2025/8jev_36200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jev_36200/06_2025/8jev_36200.map" model { file = "/net/cci-nas-00/data/ceres_data/8jev_36200/06_2025/8jev_36200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jev_36200/06_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-5710/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: 10.08, per 1000 atoms: 0.57 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: 4.91 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: 1.23 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: 8.24 Time building geometry restraints manager: 5.92 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: 0.08 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.750 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- 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 : 1.214 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: 0.5365 time to fit residues: 131.6337 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 : 1.271 ------------------------------------------------------------------------------- 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 = 0.189479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147317 restraints weight = 30394.823| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.53 r_work: 0.3776 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 2.383 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 5.15678 ( 1797) SS BOND : bond 0.00173 ( 2) SS BOND : angle 1.29730 ( 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 : 1.402 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: 0.7142 (ttt180) cc_final: 0.6933 (ttm170) REVERT: A 123 TYR cc_start: 0.6587 (t80) cc_final: 0.6157 (t80) REVERT: A 168 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7690 (p0) REVERT: A 215 ILE cc_start: 0.7780 (mt) cc_final: 0.7471 (mt) REVERT: A 357 LEU cc_start: 0.7455 (mt) cc_final: 0.7104 (mt) REVERT: A 611 MET cc_start: 0.7189 (tpt) cc_final: 0.6761 (tpp) REVERT: A 635 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7427 (ttm110) REVERT: A 658 MET cc_start: 0.7523 (ptm) cc_final: 0.7111 (ttp) REVERT: A 757 MET cc_start: 0.0055 (ptt) cc_final: -0.0416 (mmt) REVERT: B 88 PHE cc_start: 0.7353 (m-80) cc_final: 0.6979 (m-10) REVERT: B 200 GLN cc_start: 0.7381 (tt0) cc_final: 0.6365 (mm-40) REVERT: B 215 ILE cc_start: 0.7823 (mt) cc_final: 0.7509 (mt) REVERT: B 457 LYS cc_start: 0.7563 (mttm) cc_final: 0.7290 (mttm) REVERT: B 611 MET cc_start: 0.7056 (tpp) cc_final: 0.6599 (tpp) REVERT: B 658 MET cc_start: 0.7811 (ptm) cc_final: 0.7361 (ttp) REVERT: B 757 MET cc_start: 0.0378 (ttp) cc_final: -0.0139 (mmt) outliers start: 8 outliers final: 4 residues processed: 146 average time/residue: 0.5203 time to fit residues: 103.1088 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 : 1.397 ------------------------------------------------------------------------------- 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: 0.0770 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 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: 1.2144 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.185452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142919 restraints weight = 30441.785| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.53 r_work: 0.3728 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3226 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= 0.163 Angle : 0.559 17.741 12182 Z= 0.302 Chirality : 0.037 0.140 1384 Planarity : 0.005 0.052 1472 Dihedral : 3.997 15.247 1190 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 1.21 % Allowed : 8.44 % Favored : 90.35 % 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: 0.77 (0.26), residues: 1084 helix: 1.34 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS A 287 PHE 0.011 0.001 PHE B 423 TYR 0.016 0.001 TYR B 211 ARG 0.005 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 608) hydrogen bonds : angle 4.90672 ( 1797) SS BOND : bond 0.00230 ( 2) SS BOND : angle 1.32565 ( 4) covalent geometry : bond 0.00370 ( 8972) covalent geometry : angle 0.55900 (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 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.683 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: 0.6783 (t80) cc_final: 0.6302 (t80) REVERT: A 168 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 215 ILE cc_start: 0.8005 (mt) cc_final: 0.7757 (mt) REVERT: A 300 PHE cc_start: 0.6225 (m-80) cc_final: 0.5923 (m-80) REVERT: A 357 LEU cc_start: 0.7688 (mt) cc_final: 0.7369 (mt) REVERT: A 635 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7554 (ttm-80) REVERT: A 658 MET cc_start: 0.7744 (ptm) cc_final: 0.6997 (ttp) REVERT: A 757 MET cc_start: -0.0047 (ptt) cc_final: -0.0534 (mmt) REVERT: B 92 ASP cc_start: 0.5997 (t70) cc_final: 0.5620 (m-30) REVERT: B 215 ILE cc_start: 0.8060 (mt) cc_final: 0.7817 (mt) REVERT: B 457 LYS cc_start: 0.7698 (mttm) cc_final: 0.7461 (mttp) REVERT: B 611 MET cc_start: 0.7202 (tpp) cc_final: 0.6793 (tpp) REVERT: B 617 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8568 (p) REVERT: B 658 MET cc_start: 0.8046 (ptm) cc_final: 0.7697 (ptt) REVERT: B 757 MET cc_start: 0.0161 (ttp) cc_final: -0.0339 (tpt) REVERT: B 769 GLU cc_start: 0.6340 (pm20) cc_final: 0.6084 (pm20) outliers start: 11 outliers final: 4 residues processed: 146 average time/residue: 0.5930 time to fit residues: 119.4917 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 : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.184175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139951 restraints weight = 30188.823| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.67 r_work: 0.3635 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8974 Z= 0.149 Angle : 0.547 17.579 12182 Z= 0.293 Chirality : 0.037 0.135 1384 Planarity : 0.005 0.052 1472 Dihedral : 3.963 14.940 1190 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.86 % Rotamer: Outliers : 0.99 % Allowed : 10.64 % Favored : 88.38 % 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: 0.93 (0.26), residues: 1084 helix: 1.45 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.40 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.002 0.000 HIS B 633 PHE 0.008 0.001 PHE B 423 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 608) hydrogen bonds : angle 4.79879 ( 1797) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.11787 ( 4) covalent geometry : bond 0.00336 ( 8972) covalent geometry : angle 0.54647 (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 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.388 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: 0.7146 (ttt180) cc_final: 0.6844 (ttm170) REVERT: A 123 TYR cc_start: 0.6728 (t80) cc_final: 0.6261 (t80) REVERT: A 168 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7346 (p0) REVERT: A 300 PHE cc_start: 0.5937 (m-80) cc_final: 0.5559 (m-80) REVERT: A 357 LEU cc_start: 0.7278 (mt) cc_final: 0.6929 (mt) REVERT: A 635 ARG cc_start: 0.7739 (mmp80) cc_final: 0.7364 (ttm-80) REVERT: A 757 MET cc_start: -0.0055 (ptt) cc_final: -0.0554 (mmt) REVERT: B 92 ASP cc_start: 0.5710 (t70) cc_final: 0.5495 (m-30) REVERT: B 215 ILE cc_start: 0.7751 (mt) cc_final: 0.7548 (mt) REVERT: B 457 LYS cc_start: 0.7318 (mttm) cc_final: 0.7076 (mttm) REVERT: B 611 MET cc_start: 0.6791 (tpp) cc_final: 0.6378 (tpp) REVERT: B 617 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 757 MET cc_start: 0.0081 (ttp) cc_final: -0.0425 (tpt) outliers start: 9 outliers final: 5 residues processed: 144 average time/residue: 0.6169 time to fit residues: 120.6161 Evaluate side-chains 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 772 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136463 restraints weight = 30590.940| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.68 r_work: 0.3591 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8974 Z= 0.198 Angle : 0.573 17.586 12182 Z= 0.311 Chirality : 0.038 0.141 1384 Planarity : 0.005 0.055 1472 Dihedral : 4.007 15.009 1190 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.21 % Allowed : 11.62 % 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: 0.79 (0.26), residues: 1084 helix: 1.34 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.004 0.001 HIS B 633 PHE 0.013 0.001 PHE A 423 TYR 0.015 0.001 TYR B 211 ARG 0.005 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 608) hydrogen bonds : angle 4.88359 ( 1797) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.39196 ( 4) covalent geometry : bond 0.00458 ( 8972) covalent geometry : angle 0.57300 (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 149 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 1.326 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: 0.6819 (t80) cc_final: 0.6240 (t80) REVERT: A 168 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7199 (p0) REVERT: A 635 ARG cc_start: 0.7741 (mmp80) cc_final: 0.7405 (ttm-80) REVERT: A 757 MET cc_start: -0.0207 (ptt) cc_final: -0.0676 (mmt) REVERT: B 457 LYS cc_start: 0.7384 (mttm) cc_final: 0.7063 (mttm) REVERT: B 611 MET cc_start: 0.6927 (tpp) cc_final: 0.6553 (tpp) REVERT: B 617 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 757 MET cc_start: 0.0397 (ttp) cc_final: -0.0360 (tpt) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.5414 time to fit residues: 108.3156 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 : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 617 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143690 restraints weight = 29480.874| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.31 r_work: 0.3581 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4096 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= 0.177 Angle : 0.557 17.572 12182 Z= 0.300 Chirality : 0.037 0.137 1384 Planarity : 0.005 0.068 1472 Dihedral : 3.978 14.852 1190 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.43 % Allowed : 12.83 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS B 633 PHE 0.012 0.001 PHE B 335 TYR 0.014 0.001 TYR A 211 ARG 0.010 0.001 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 608) hydrogen bonds : angle 4.80022 ( 1797) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.19289 ( 4) covalent geometry : bond 0.00407 ( 8972) covalent geometry : angle 0.55658 (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 143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.916 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: 0.7716 (OUTLIER) cc_final: 0.7461 (p0) REVERT: A 546 GLU cc_start: 0.6802 (tt0) cc_final: 0.6568 (tt0) REVERT: A 635 ARG cc_start: 0.7874 (mmp80) cc_final: 0.7473 (ttm-80) REVERT: A 757 MET cc_start: -0.0272 (ptt) cc_final: -0.0769 (mmp) REVERT: B 611 MET cc_start: 0.7106 (tpp) cc_final: 0.6762 (tpp) REVERT: B 617 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 757 MET cc_start: 0.0280 (ttp) cc_final: -0.0482 (tpt) REVERT: B 769 GLU cc_start: 0.6540 (pm20) cc_final: 0.5901 (mm-30) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 0.6616 time to fit residues: 129.4982 Evaluate side-chains 136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.182395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142893 restraints weight = 29642.030| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.15 r_work: 0.3613 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8974 Z= 0.175 Angle : 0.555 17.681 12182 Z= 0.300 Chirality : 0.037 0.136 1384 Planarity : 0.005 0.060 1472 Dihedral : 3.945 14.548 1190 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.43 % Allowed : 12.61 % 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: 0.91 (0.26), residues: 1084 helix: 1.44 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.43 (0.33), 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 0.010 0.001 PHE B 335 TYR 0.013 0.001 TYR B 211 ARG 0.009 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 608) hydrogen bonds : angle 4.77082 ( 1797) SS BOND : bond 0.00225 ( 2) SS BOND : angle 1.19688 ( 4) covalent geometry : bond 0.00399 ( 8972) covalent geometry : angle 0.55513 (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 145 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.560 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: 0.7658 (OUTLIER) cc_final: 0.7387 (p0) REVERT: A 546 GLU cc_start: 0.6863 (tt0) cc_final: 0.6647 (tt0) REVERT: A 635 ARG cc_start: 0.7837 (mmp80) cc_final: 0.7358 (ttm-80) REVERT: A 757 MET cc_start: -0.0367 (ptt) cc_final: -0.0849 (mmp) REVERT: A 782 GLN cc_start: 0.7801 (pm20) cc_final: 0.7465 (pt0) REVERT: B 611 MET cc_start: 0.7056 (tpp) cc_final: 0.6738 (tpp) REVERT: B 617 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 757 MET cc_start: 0.0418 (ttp) cc_final: -0.0661 (tpp) REVERT: B 769 GLU cc_start: 0.6577 (pm20) cc_final: 0.5889 (mm-30) outliers start: 13 outliers final: 11 residues processed: 141 average time/residue: 0.5192 time to fit residues: 100.9185 Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.183022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138866 restraints weight = 29485.375| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.67 r_work: 0.3556 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4394 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= 0.138 Angle : 0.528 17.684 12182 Z= 0.284 Chirality : 0.036 0.130 1384 Planarity : 0.005 0.067 1472 Dihedral : 3.848 14.202 1190 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.32 % Allowed : 12.94 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.26), residues: 1084 helix: 1.62 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 324 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 0.011 0.001 PHE B 335 TYR 0.013 0.001 TYR B 550 ARG 0.012 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 608) hydrogen bonds : angle 4.65463 ( 1797) SS BOND : bond 0.00090 ( 2) SS BOND : angle 1.00041 ( 4) covalent geometry : bond 0.00307 ( 8972) covalent geometry : angle 0.52821 (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 140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.283 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: 0.7053 (OUTLIER) cc_final: 0.6769 (p0) REVERT: A 300 PHE cc_start: 0.5643 (m-80) cc_final: 0.5247 (m-80) REVERT: A 350 TRP cc_start: 0.7193 (m100) cc_final: 0.6965 (m100) REVERT: A 635 ARG cc_start: 0.7776 (mmp80) cc_final: 0.7086 (ttm-80) REVERT: A 757 MET cc_start: -0.0539 (ptt) cc_final: -0.1055 (mmt) REVERT: A 782 GLN cc_start: 0.7470 (pm20) cc_final: 0.7231 (pt0) REVERT: B 611 MET cc_start: 0.6471 (tpp) cc_final: 0.6146 (tpp) REVERT: B 617 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 757 MET cc_start: 0.0019 (ttp) cc_final: -0.0994 (tpp) REVERT: B 769 GLU cc_start: 0.6269 (pm20) cc_final: 0.5759 (mm-30) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.5021 time to fit residues: 92.7418 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 : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain 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 636 LEU 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: 0.6980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.182051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139922 restraints weight = 29885.384| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.57 r_work: 0.3653 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8974 Z= 0.120 Angle : 0.517 17.828 12182 Z= 0.276 Chirality : 0.036 0.128 1384 Planarity : 0.004 0.053 1472 Dihedral : 3.739 14.262 1190 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.10 % Allowed : 13.49 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.26), residues: 1084 helix: 1.79 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 322 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 0.010 0.001 PHE B 335 TYR 0.013 0.001 TYR B 550 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 608) hydrogen bonds : angle 4.54111 ( 1797) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.93137 ( 4) covalent geometry : bond 0.00260 ( 8972) covalent geometry : angle 0.51633 (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 136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.354 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: 0.7343 (OUTLIER) cc_final: 0.7063 (p0) REVERT: A 350 TRP cc_start: 0.7377 (m100) cc_final: 0.7155 (m100) REVERT: A 635 ARG cc_start: 0.7810 (mmp80) cc_final: 0.7199 (ttm-80) REVERT: A 757 MET cc_start: -0.0270 (ptt) cc_final: -0.0849 (mmt) REVERT: A 782 GLN cc_start: 0.7632 (pm20) cc_final: 0.7398 (pt0) REVERT: B 611 MET cc_start: 0.6765 (tpp) cc_final: 0.6475 (tpp) REVERT: B 617 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8361 (p) REVERT: B 769 GLU cc_start: 0.6245 (pm20) cc_final: 0.6019 (mm-30) REVERT: B 782 GLN cc_start: 0.8203 (pm20) cc_final: 0.7845 (pt0) outliers start: 10 outliers final: 8 residues processed: 132 average time/residue: 0.5111 time to fit residues: 91.4988 Evaluate side-chains 130 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 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: 1.9990 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 0.0010 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138946 restraints weight = 29452.422| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.67 r_work: 0.3570 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8974 Z= 0.138 Angle : 0.528 17.780 12182 Z= 0.283 Chirality : 0.036 0.131 1384 Planarity : 0.005 0.102 1472 Dihedral : 3.777 14.734 1190 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.32 % Allowed : 13.38 % Favored : 85.31 % 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: 1.37 (0.26), residues: 1084 helix: 1.76 (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 A 152 HIS 0.003 0.000 HIS B 633 PHE 0.010 0.001 PHE B 335 TYR 0.013 0.001 TYR B 550 ARG 0.003 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 608) hydrogen bonds : angle 4.55461 ( 1797) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.98715 ( 4) covalent geometry : bond 0.00306 ( 8972) covalent geometry : angle 0.52796 (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 133 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.251 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 95 ARG cc_start: 0.6710 (ttt180) cc_final: 0.6378 (ttm170) REVERT: A 168 ASN cc_start: 0.6938 (OUTLIER) cc_final: 0.6621 (p0) REVERT: A 635 ARG cc_start: 0.7650 (mmp80) cc_final: 0.6959 (ttm-80) REVERT: A 757 MET cc_start: -0.0415 (ptt) cc_final: -0.0975 (mmt) REVERT: A 782 GLN cc_start: 0.7401 (pm20) cc_final: 0.7154 (pt0) REVERT: B 611 MET cc_start: 0.6418 (tpp) cc_final: 0.6125 (tpp) REVERT: B 617 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 769 GLU cc_start: 0.6423 (pm20) cc_final: 0.5991 (mm-30) REVERT: B 782 GLN cc_start: 0.8115 (pm20) cc_final: 0.7822 (pt0) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.5292 time to fit residues: 91.8982 Evaluate side-chains 129 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0494 > 50: distance: 68 - 85: 3.177 distance: 85 - 86: 3.789 distance: 85 - 93: 3.425 distance: 86 - 87: 3.238 distance: 86 - 89: 6.112 distance: 86 - 94: 3.288 distance: 87 - 99: 3.602 distance: 88 - 139: 6.304 distance: 89 - 90: 3.756 distance: 89 - 95: 4.607 distance: 90 - 92: 5.969 distance: 92 - 97: 3.818 distance: 92 - 98: 4.209 distance: 100 - 101: 4.098 distance: 100 - 103: 3.733 distance: 102 - 158: 5.302 distance: 103 - 104: 4.056 distance: 103 - 105: 4.377 distance: 103 - 108: 3.386 distance: 104 - 109: 3.550 distance: 105 - 110: 4.637 distance: 105 - 111: 3.818 distance: 105 - 112: 4.699 distance: 114 - 115: 3.101 distance: 114 - 120: 4.278 distance: 115 - 116: 7.303 distance: 115 - 124: 4.834 distance: 116 - 177: 6.511 distance: 117 - 118: 5.546 distance: 117 - 121: 5.579 distance: 118 - 123: 5.518 distance: 124 - 125: 3.639 distance: 126 - 139: 4.027 distance: 127 - 199: 5.537 distance: 128 - 135: 3.039 distance: 130 - 131: 3.441 distance: 139 - 147: 3.565 distance: 141 - 142: 4.739 distance: 141 - 158: 3.372 distance: 142 - 214: 8.086 distance: 143 - 144: 5.941 distance: 143 - 149: 3.347 distance: 143 - 150: 3.709 distance: 144 - 145: 3.823 distance: 145 - 152: 4.092 distance: 145 - 153: 3.871 distance: 145 - 154: 4.645 distance: 158 - 166: 6.101 distance: 160 - 161: 4.456 distance: 161 - 233: 4.585 distance: 162 - 164: 4.180 distance: 162 - 168: 6.209 distance: 163 - 169: 3.453 distance: 164 - 173: 4.409 distance: 165 - 174: 8.663 distance: 165 - 175: 12.002 distance: 165 - 176: 8.970 distance: 177 - 186: 3.092 distance: 178 - 179: 4.865 distance: 178 - 181: 5.528 distance: 178 - 187: 6.546 distance: 179 - 180: 4.696 distance: 179 - 199: 5.340 distance: 181 - 188: 4.818 distance: 182 - 190: 3.527 distance: 184 - 185: 3.921 distance: 199 - 200: 6.831 distance: 199 - 208: 4.624 distance: 200 - 201: 3.910 distance: 200 - 203: 8.679 distance: 200 - 209: 7.399 distance: 201 - 202: 22.318 distance: 201 - 214: 10.631 distance: 203 - 204: 6.133 distance: 203 - 210: 5.131 distance: 203 - 211: 4.913 distance: 204 - 205: 4.280 distance: 204 - 212: 8.060 distance: 204 - 213: 7.467 distance: 205 - 206: 3.980 distance: 205 - 207: 6.086 distance: 214 - 215: 6.346 distance: 214 - 222: 30.876 distance: 215 - 216: 11.731 distance: 215 - 218: 6.340 distance: 215 - 223: 7.768 distance: 216 - 217: 14.600 distance: 216 - 233: 6.631 distance: 218 - 219: 5.478 distance: 218 - 224: 4.142 distance: 218 - 225: 5.560 distance: 219 - 220: 5.463 distance: 219 - 221: 6.272 distance: 219 - 226: 4.267 distance: 220 - 227: 5.288 distance: 220 - 228: 5.302 distance: 220 - 229: 4.069 distance: 221 - 231: 4.262 distance: 233 - 234: 6.610 distance: 233 - 244: 3.635 distance: 234 - 237: 10.571 distance: 234 - 245: 6.802 distance: 235 - 236: 4.180 distance: 237 - 238: 4.191 distance: 237 - 246: 4.717 distance: 238 - 239: 6.218 distance: 238 - 240: 3.175 distance: 239 - 241: 3.226 distance: 239 - 248: 3.117 distance: 240 - 242: 3.124 distance: 240 - 249: 5.151 distance: 241 - 243: 4.742 distance: 241 - 250: 4.174 distance: 242 - 243: 6.365 distance: 242 - 251: 3.648 distance: 243 - 252: 3.401