Starting phenix.real_space_refine on Sun Apr 27 04:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6t_39804/04_2025/8z6t_39804.cif" } resolution = 2.92 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2888 2.51 5 N 750 2.21 5 O 865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4526 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1558 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "C" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1424 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain breaks: 4 Chain: "B" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1544 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 10, 'TRANS': 191} Chain breaks: 3 Time building chain proxies: 3.82, per 1000 atoms: 0.84 Number of scatterers: 4526 At special positions: 0 Unit cell: (96.928, 71.764, 114.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 865 8.00 N 750 7.00 C 2888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 569.0 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 10.2% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.551A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.781A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.390A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 202 through 209 removed outlier: 4.055A pdb=" N HIS C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.017A pdb=" N GLN B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.721A pdb=" N THR B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.564A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.391A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.893A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL C 39 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR C 55 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP C 41 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.893A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.522A pdb=" N LEU C 89 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.514A pdb=" N VAL C 154 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR C 193 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 181 " --> pdb=" O TYR C 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.665A pdb=" N SER C 213 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.560A pdb=" N THR B 77 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.359A pdb=" N ILE B 39 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE B 55 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP B 41 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 64 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.852A pdb=" N TYR B 117 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 135 through 138 removed outlier: 3.875A pdb=" N SER B 195 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 159 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 191 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.576A pdb=" N THR B 166 " --> pdb=" O ASN B 214 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 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: 1.41 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 757 1.32 - 1.44: 1328 1.44 - 1.57: 2532 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 4646 Sorted by residual: bond pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.04e-02 9.25e+03 3.31e+01 bond pdb=" CA LEU B 110 " pdb=" C LEU B 110 " ideal model delta sigma weight residual 1.527 1.472 0.055 1.21e-02 6.83e+03 2.05e+01 bond pdb=" CA SER A 443 " pdb=" CB SER A 443 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.48e-02 4.57e+03 1.98e+01 bond pdb=" CA THR A 346 " pdb=" C THR A 346 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.21e-02 6.83e+03 1.77e+01 bond pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta sigma weight residual 1.532 1.461 0.070 1.69e-02 3.50e+03 1.73e+01 ... (remaining 4641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6151 1.64 - 3.28: 118 3.28 - 4.92: 38 4.92 - 6.56: 8 6.56 - 8.20: 5 Bond angle restraints: 6320 Sorted by residual: angle pdb=" C SER A 443 " pdb=" CA SER A 443 " pdb=" CB SER A 443 " ideal model delta sigma weight residual 111.43 104.78 6.65 1.24e+00 6.50e-01 2.88e+01 angle pdb=" N PHE A 347 " pdb=" CA PHE A 347 " pdb=" C PHE A 347 " ideal model delta sigma weight residual 109.80 101.60 8.20 1.70e+00 3.46e-01 2.33e+01 angle pdb=" N SER A 443 " pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 107.20 114.04 -6.84 1.70e+00 3.46e-01 1.62e+01 angle pdb=" C ARG C 8 " pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta sigma weight residual 122.62 116.52 6.10 1.56e+00 4.11e-01 1.53e+01 angle pdb=" N THR A 346 " pdb=" CA THR A 346 " pdb=" C THR A 346 " ideal model delta sigma weight residual 109.50 103.78 5.72 1.58e+00 4.01e-01 1.31e+01 ... (remaining 6315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 2580 11.92 - 23.84: 105 23.84 - 35.76: 29 35.76 - 47.68: 17 47.68 - 59.60: 9 Dihedral angle restraints: 2740 sinusoidal: 1044 harmonic: 1696 Sorted by residual: dihedral pdb=" CA ASP C 56 " pdb=" C ASP C 56 " pdb=" N VAL C 57 " pdb=" CA VAL C 57 " ideal model delta harmonic sigma weight residual 180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" N PHE A 347 " pdb=" C PHE A 347 " pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta harmonic sigma weight residual 122.80 114.00 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C PHE A 347 " pdb=" N PHE A 347 " pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta harmonic sigma weight residual -122.60 -114.30 -8.30 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 2737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 561 0.048 - 0.097: 71 0.097 - 0.145: 52 0.145 - 0.193: 4 0.193 - 0.241: 3 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA GLN B 107 " pdb=" N GLN B 107 " pdb=" C GLN B 107 " pdb=" CB GLN B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA THR A 345 " pdb=" N THR A 345 " pdb=" C THR A 345 " pdb=" CB THR A 345 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP B 112A" pdb=" N ASP B 112A" pdb=" C ASP B 112A" pdb=" CB ASP B 112A" both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 688 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 344 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ALA A 344 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 344 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 345 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 105 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ALA B 105 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA B 105 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 106 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 444 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 445 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.019 5.00e-02 4.00e+02 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 346 2.74 - 3.28: 4369 3.28 - 3.82: 7167 3.82 - 4.36: 8706 4.36 - 4.90: 15100 Nonbonded interactions: 35688 Sorted by model distance: nonbonded pdb=" O VAL C 126 " pdb=" OH TYR C 161 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 186 " pdb=" N ALA C 194 " model vdw 2.200 3.120 nonbonded pdb=" ND1 HIS B 215 " pdb=" OG SER B 218 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.225 3.040 nonbonded pdb=" O ASP C 56 " pdb=" N LYS C 66 " model vdw 2.235 3.120 ... (remaining 35683 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.580 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:15.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.005 0.070 4653 Z= 0.322 Angle : 0.627 8.199 6334 Z= 0.360 Chirality : 0.048 0.241 691 Planarity : 0.003 0.035 802 Dihedral : 8.846 59.602 1639 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.27 % Favored : 94.38 % Rotamer: Outliers : 3.78 % Allowed : 4.38 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.32), residues: 569 helix: -3.03 (0.59), residues: 47 sheet: -0.96 (0.38), residues: 185 loop : -2.40 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.000 HIS A 339 PHE 0.016 0.001 PHE A 347 TYR 0.006 0.001 TYR B 57 ARG 0.001 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.27842 ( 139) hydrogen bonds : angle 10.32319 ( 369) SS BOND : bond 0.00134 ( 7) SS BOND : angle 0.46125 ( 14) covalent geometry : bond 0.00473 ( 4646) covalent geometry : angle 0.62694 ( 6320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.532 Fit side-chains REVERT: A 346 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7753 (p) REVERT: A 360 ASN cc_start: 0.7887 (m110) cc_final: 0.7660 (m110) REVERT: A 362 VAL cc_start: 0.7998 (m) cc_final: 0.7797 (p) REVERT: A 399 SER cc_start: 0.8104 (m) cc_final: 0.7858 (p) REVERT: A 406 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: A 439 ASN cc_start: 0.7743 (t0) cc_final: 0.7253 (t0) REVERT: A 442 ASP cc_start: 0.7741 (m-30) cc_final: 0.7279 (m-30) REVERT: A 443 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.7795 (p) REVERT: A 455 LEU cc_start: 0.7720 (tp) cc_final: 0.7313 (tp) REVERT: A 456 PHE cc_start: 0.7775 (m-10) cc_final: 0.7494 (m-10) REVERT: A 494 SER cc_start: 0.7968 (t) cc_final: 0.7759 (p) REVERT: C 30 VAL cc_start: 0.8024 (t) cc_final: 0.7778 (m) REVERT: B 117 TYR cc_start: 0.7726 (m-80) cc_final: 0.6957 (m-80) REVERT: B 184 VAL cc_start: 0.7654 (t) cc_final: 0.7422 (m) REVERT: B 193 LEU cc_start: 0.7741 (pt) cc_final: 0.7449 (pt) outliers start: 19 outliers final: 4 residues processed: 148 average time/residue: 0.6339 time to fit residues: 100.2217 Evaluate side-chains 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 450 ASN A 474 GLN C 95 GLN B 3 GLN B 6 GLN B 107 GLN B 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122629 restraints weight = 6450.242| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.05 r_work: 0.3548 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4653 Z= 0.148 Angle : 0.605 6.528 6334 Z= 0.305 Chirality : 0.046 0.160 691 Planarity : 0.005 0.045 802 Dihedral : 5.940 55.281 644 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.18 % Allowed : 14.54 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.73 (0.33), residues: 569 helix: -2.72 (0.65), residues: 42 sheet: -0.23 (0.36), residues: 195 loop : -1.54 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.011 0.001 PHE A 429 TYR 0.012 0.001 TYR B 67 ARG 0.003 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 139) hydrogen bonds : angle 6.32697 ( 369) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.58623 ( 14) covalent geometry : bond 0.00339 ( 4646) covalent geometry : angle 0.60518 ( 6320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.384 Fit side-chains REVERT: A 374 PHE cc_start: 0.8210 (m-80) cc_final: 0.7952 (m-80) REVERT: A 442 ASP cc_start: 0.7939 (m-30) cc_final: 0.7570 (m-30) REVERT: A 456 PHE cc_start: 0.8093 (m-10) cc_final: 0.7869 (m-10) REVERT: C 29 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: C 201 LEU cc_start: 0.7272 (mt) cc_final: 0.7000 (tm) REVERT: B 22 SER cc_start: 0.7901 (p) cc_final: 0.7603 (t) REVERT: B 37 TYR cc_start: 0.8306 (m-80) cc_final: 0.8106 (m-80) REVERT: B 95 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8486 (mtpp) REVERT: B 156 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5924 (tt) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.4580 time to fit residues: 58.0746 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 409 GLN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121471 restraints weight = 6486.183| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.02 r_work: 0.3537 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4653 Z= 0.111 Angle : 0.557 6.181 6334 Z= 0.274 Chirality : 0.044 0.153 691 Planarity : 0.004 0.040 802 Dihedral : 5.187 48.674 639 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.58 % Allowed : 14.94 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.34), residues: 569 helix: -2.46 (0.79), residues: 35 sheet: 0.26 (0.37), residues: 190 loop : -1.26 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 52 HIS 0.003 0.000 HIS B 215 PHE 0.007 0.001 PHE C 160 TYR 0.009 0.001 TYR C 38 ARG 0.002 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 139) hydrogen bonds : angle 5.65662 ( 369) SS BOND : bond 0.00221 ( 7) SS BOND : angle 0.41377 ( 14) covalent geometry : bond 0.00255 ( 4646) covalent geometry : angle 0.55747 ( 6320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.485 Fit side-chains REVERT: A 374 PHE cc_start: 0.8201 (m-80) cc_final: 0.7929 (m-80) REVERT: A 405 ASN cc_start: 0.8107 (p0) cc_final: 0.7893 (p0) REVERT: A 442 ASP cc_start: 0.8031 (m-30) cc_final: 0.7617 (m-30) REVERT: A 492 LEU cc_start: 0.7997 (mp) cc_final: 0.7787 (mt) REVERT: A 517 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6158 (mp) REVERT: B 21 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7637 (tt) REVERT: B 95 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8599 (mtpp) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 0.4582 time to fit residues: 55.2733 Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 55 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.138285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116495 restraints weight = 6468.965| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.99 r_work: 0.3468 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4653 Z= 0.193 Angle : 0.641 9.981 6334 Z= 0.314 Chirality : 0.046 0.169 691 Planarity : 0.005 0.040 802 Dihedral : 5.500 47.244 639 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.57 % Allowed : 17.73 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.99 (0.34), residues: 569 helix: -2.41 (0.80), residues: 35 sheet: 0.48 (0.38), residues: 190 loop : -1.17 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.013 0.002 PHE A 456 TYR 0.019 0.002 TYR C 38 ARG 0.003 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 139) hydrogen bonds : angle 5.67408 ( 369) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.66002 ( 14) covalent geometry : bond 0.00447 ( 4646) covalent geometry : angle 0.64140 ( 6320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.430 Fit side-chains REVERT: A 374 PHE cc_start: 0.8227 (m-80) cc_final: 0.7926 (m-80) REVERT: A 385 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 438 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7528 (t) REVERT: A 442 ASP cc_start: 0.8064 (m-30) cc_final: 0.7624 (m-30) REVERT: A 446 SER cc_start: 0.8491 (p) cc_final: 0.8272 (m) REVERT: A 492 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (mt) REVERT: A 517 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 528 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7614 (ttmt) REVERT: C 28 SER cc_start: 0.8257 (m) cc_final: 0.7947 (p) REVERT: C 29 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: B 23 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7580 (t) REVERT: B 126 VAL cc_start: 0.8654 (t) cc_final: 0.8323 (m) REVERT: B 180 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8223 (p) outliers start: 33 outliers final: 17 residues processed: 94 average time/residue: 0.4208 time to fit residues: 43.6099 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116370 restraints weight = 6596.212| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.02 r_work: 0.3464 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4653 Z= 0.158 Angle : 0.600 8.475 6334 Z= 0.294 Chirality : 0.045 0.145 691 Planarity : 0.005 0.037 802 Dihedral : 5.236 45.629 638 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.37 % Allowed : 17.93 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.84 (0.35), residues: 569 helix: -2.27 (0.83), residues: 35 sheet: 0.59 (0.38), residues: 190 loop : -1.07 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.010 0.001 PHE A 456 TYR 0.015 0.001 TYR C 38 ARG 0.003 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 139) hydrogen bonds : angle 5.50933 ( 369) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.57758 ( 14) covalent geometry : bond 0.00370 ( 4646) covalent geometry : angle 0.60013 ( 6320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.457 Fit side-chains REVERT: A 374 PHE cc_start: 0.8178 (m-80) cc_final: 0.7806 (m-80) REVERT: A 438 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7564 (t) REVERT: A 442 ASP cc_start: 0.8115 (m-30) cc_final: 0.7708 (m-30) REVERT: A 443 SER cc_start: 0.8365 (m) cc_final: 0.8078 (m) REVERT: A 446 SER cc_start: 0.8470 (p) cc_final: 0.8233 (m) REVERT: A 492 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 517 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6486 (mp) REVERT: A 528 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7575 (ttmt) REVERT: C 29 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: C 196 SER cc_start: 0.7708 (t) cc_final: 0.7493 (t) REVERT: B 23 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 126 VAL cc_start: 0.8667 (t) cc_final: 0.8337 (m) REVERT: B 180 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 220 THR cc_start: 0.8459 (m) cc_final: 0.7676 (p) outliers start: 32 outliers final: 20 residues processed: 93 average time/residue: 0.4835 time to fit residues: 49.3049 Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3861 r_free = 0.3861 target = 0.137930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116266 restraints weight = 6473.359| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.01 r_work: 0.3460 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4653 Z= 0.157 Angle : 0.591 8.514 6334 Z= 0.291 Chirality : 0.045 0.144 691 Planarity : 0.005 0.036 802 Dihedral : 5.330 48.400 638 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.97 % Allowed : 17.73 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.72 (0.35), residues: 569 helix: -2.26 (0.83), residues: 35 sheet: 0.69 (0.39), residues: 190 loop : -1.00 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.010 0.001 PHE A 429 TYR 0.016 0.001 TYR C 38 ARG 0.003 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 139) hydrogen bonds : angle 5.46568 ( 369) SS BOND : bond 0.00198 ( 7) SS BOND : angle 0.53060 ( 14) covalent geometry : bond 0.00369 ( 4646) covalent geometry : angle 0.59157 ( 6320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.475 Fit side-chains REVERT: A 438 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7585 (t) REVERT: A 442 ASP cc_start: 0.8082 (m-30) cc_final: 0.7722 (m-30) REVERT: A 443 SER cc_start: 0.8491 (m) cc_final: 0.8225 (m) REVERT: A 446 SER cc_start: 0.8486 (p) cc_final: 0.8256 (m) REVERT: A 492 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 517 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6629 (mp) REVERT: A 528 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7560 (ttmt) REVERT: C 29 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: C 196 SER cc_start: 0.7727 (t) cc_final: 0.7502 (t) REVERT: B 23 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (t) REVERT: B 180 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 220 THR cc_start: 0.8443 (m) cc_final: 0.7710 (p) outliers start: 35 outliers final: 26 residues processed: 95 average time/residue: 0.4690 time to fit residues: 48.9405 Evaluate side-chains 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** 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 = 0.3845 r_free = 0.3845 target = 0.136699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114978 restraints weight = 6446.830| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.99 r_work: 0.3429 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4653 Z= 0.197 Angle : 0.624 9.204 6334 Z= 0.308 Chirality : 0.046 0.155 691 Planarity : 0.005 0.037 802 Dihedral : 5.548 50.602 638 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 7.17 % Allowed : 17.33 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.36), residues: 569 helix: -2.30 (0.83), residues: 35 sheet: 0.65 (0.39), residues: 190 loop : -1.04 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.013 0.002 PHE A 429 TYR 0.017 0.001 TYR C 38 ARG 0.003 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 139) hydrogen bonds : angle 5.58478 ( 369) SS BOND : bond 0.00216 ( 7) SS BOND : angle 0.53171 ( 14) covalent geometry : bond 0.00460 ( 4646) covalent geometry : angle 0.62433 ( 6320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.509 Fit side-chains REVERT: A 374 PHE cc_start: 0.8187 (m-80) cc_final: 0.7837 (m-80) REVERT: A 385 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8490 (p) REVERT: A 438 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 442 ASP cc_start: 0.8075 (m-30) cc_final: 0.7719 (m-30) REVERT: A 443 SER cc_start: 0.8485 (m) cc_final: 0.8209 (m) REVERT: A 446 SER cc_start: 0.8518 (p) cc_final: 0.8254 (m) REVERT: A 473 TYR cc_start: 0.7618 (t80) cc_final: 0.7017 (t80) REVERT: A 492 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7707 (mt) REVERT: A 517 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6776 (mp) REVERT: A 528 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7551 (ttmt) REVERT: C 28 SER cc_start: 0.8319 (m) cc_final: 0.7965 (p) REVERT: C 98 ASP cc_start: 0.7819 (m-30) cc_final: 0.7501 (m-30) REVERT: B 23 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7633 (t) outliers start: 36 outliers final: 23 residues processed: 98 average time/residue: 0.4897 time to fit residues: 52.5692 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.136536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114830 restraints weight = 6491.085| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.00 r_work: 0.3426 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4653 Z= 0.190 Angle : 0.616 10.104 6334 Z= 0.303 Chirality : 0.046 0.147 691 Planarity : 0.005 0.036 802 Dihedral : 5.565 50.613 638 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.57 % Allowed : 17.53 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.36), residues: 569 helix: -2.33 (0.82), residues: 35 sheet: 0.73 (0.39), residues: 190 loop : -1.02 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.019 0.002 PHE A 456 TYR 0.017 0.001 TYR C 38 ARG 0.003 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 139) hydrogen bonds : angle 5.52627 ( 369) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.52563 ( 14) covalent geometry : bond 0.00445 ( 4646) covalent geometry : angle 0.61636 ( 6320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.486 Fit side-chains REVERT: A 345 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 367 VAL cc_start: 0.8499 (m) cc_final: 0.8201 (p) REVERT: A 385 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 438 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7589 (t) REVERT: A 442 ASP cc_start: 0.8073 (m-30) cc_final: 0.7736 (m-30) REVERT: A 443 SER cc_start: 0.8490 (m) cc_final: 0.8216 (m) REVERT: A 446 SER cc_start: 0.8531 (p) cc_final: 0.8281 (m) REVERT: A 492 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7701 (mt) REVERT: A 517 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 528 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7547 (ttmt) REVERT: C 29 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: C 98 ASP cc_start: 0.7824 (m-30) cc_final: 0.7513 (m-30) REVERT: C 196 SER cc_start: 0.7802 (t) cc_final: 0.7582 (t) REVERT: B 23 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7665 (t) outliers start: 33 outliers final: 23 residues processed: 100 average time/residue: 0.4513 time to fit residues: 49.5875 Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.138311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116644 restraints weight = 6480.512| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.98 r_work: 0.3452 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4653 Z= 0.128 Angle : 0.592 9.552 6334 Z= 0.285 Chirality : 0.044 0.143 691 Planarity : 0.004 0.037 802 Dihedral : 5.378 50.427 638 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.58 % Allowed : 18.92 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.57 (0.36), residues: 569 helix: -2.35 (0.83), residues: 35 sheet: 0.86 (0.40), residues: 190 loop : -0.91 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.023 0.001 PHE A 456 TYR 0.012 0.001 TYR A 473 ARG 0.002 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 139) hydrogen bonds : angle 5.35333 ( 369) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.51024 ( 14) covalent geometry : bond 0.00304 ( 4646) covalent geometry : angle 0.59224 ( 6320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.488 Fit side-chains REVERT: A 345 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8018 (m) REVERT: A 438 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7593 (t) REVERT: A 439 ASN cc_start: 0.8294 (t0) cc_final: 0.7927 (t160) REVERT: A 442 ASP cc_start: 0.8060 (m-30) cc_final: 0.7753 (m-30) REVERT: A 443 SER cc_start: 0.8450 (m) cc_final: 0.8162 (m) REVERT: A 446 SER cc_start: 0.8444 (p) cc_final: 0.8181 (m) REVERT: A 473 TYR cc_start: 0.7578 (t80) cc_final: 0.7063 (t80) REVERT: A 492 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7711 (mt) REVERT: A 517 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6754 (mp) REVERT: A 528 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7517 (ttmt) REVERT: C 29 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: C 98 ASP cc_start: 0.7782 (m-30) cc_final: 0.7483 (m-30) REVERT: C 196 SER cc_start: 0.7824 (t) cc_final: 0.7596 (t) REVERT: B 23 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7603 (t) outliers start: 28 outliers final: 21 residues processed: 101 average time/residue: 0.4987 time to fit residues: 54.9375 Evaluate side-chains 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 448 ASN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116113 restraints weight = 6499.920| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.98 r_work: 0.3437 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4653 Z= 0.151 Angle : 0.605 9.836 6334 Z= 0.292 Chirality : 0.045 0.143 691 Planarity : 0.004 0.036 802 Dihedral : 5.416 49.466 638 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.78 % Allowed : 19.32 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.55 (0.37), residues: 569 helix: -2.28 (0.85), residues: 35 sheet: 0.88 (0.40), residues: 192 loop : -0.92 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.028 0.002 PHE A 456 TYR 0.015 0.001 TYR C 38 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 139) hydrogen bonds : angle 5.35272 ( 369) SS BOND : bond 0.00144 ( 7) SS BOND : angle 0.47086 ( 14) covalent geometry : bond 0.00357 ( 4646) covalent geometry : angle 0.60496 ( 6320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.476 Fit side-chains REVERT: A 345 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8044 (m) REVERT: A 438 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 439 ASN cc_start: 0.8304 (t0) cc_final: 0.7945 (t160) REVERT: A 442 ASP cc_start: 0.8098 (m-30) cc_final: 0.7797 (m-30) REVERT: A 443 SER cc_start: 0.8459 (m) cc_final: 0.8202 (m) REVERT: A 446 SER cc_start: 0.8478 (p) cc_final: 0.8238 (m) REVERT: A 492 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7711 (mt) REVERT: A 494 SER cc_start: 0.8339 (m) cc_final: 0.7866 (p) REVERT: A 517 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6804 (mp) REVERT: A 528 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7537 (ttmt) REVERT: C 29 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: C 98 ASP cc_start: 0.7785 (m-30) cc_final: 0.7481 (m-30) REVERT: C 196 SER cc_start: 0.7820 (t) cc_final: 0.7596 (t) outliers start: 29 outliers final: 23 residues processed: 96 average time/residue: 0.4459 time to fit residues: 47.1626 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 120 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.138691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116965 restraints weight = 6405.219| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.01 r_work: 0.3447 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4653 Z= 0.126 Angle : 0.589 9.172 6334 Z= 0.284 Chirality : 0.044 0.143 691 Planarity : 0.004 0.037 802 Dihedral : 5.335 49.896 638 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.38 % Allowed : 19.72 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.47 (0.37), residues: 569 helix: -2.27 (0.85), residues: 35 sheet: 0.89 (0.39), residues: 195 loop : -0.84 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.029 0.001 PHE A 456 TYR 0.016 0.001 TYR A 473 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 139) hydrogen bonds : angle 5.33443 ( 369) SS BOND : bond 0.00129 ( 7) SS BOND : angle 0.50129 ( 14) covalent geometry : bond 0.00299 ( 4646) covalent geometry : angle 0.58952 ( 6320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.58 seconds wall clock time: 65 minutes 25.02 seconds (3925.02 seconds total)