Starting phenix.real_space_refine on Thu Mar 6 04:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.map" model { file = "/net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h7z_34526/03_2025/8h7z_34526.cif" } resolution = 3.07 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= 0.105 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 22 5.16 5 C 3109 2.51 5 N 813 2.21 5 O 941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4885 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "F" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Time building chain proxies: 3.65, per 1000 atoms: 0.75 Number of scatterers: 4885 At special positions: 0 Unit cell: (66.8, 64.128, 134.936, 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 22 16.00 O 941 8.00 N 813 7.00 C 3109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 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: 1.24 Conformation dependent library (CDL) restraints added in 627.0 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 16 sheets defined 11.6% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.180A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.589A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.536A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.529A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.507A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.571A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.692A pdb=" N ALA I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.525A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.884A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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 'F' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.807A pdb=" N ARG F 98 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.765A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.765A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 164 removed outlier: 3.661A pdb=" N VAL F 208 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL F 217 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS F 210 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.662A pdb=" N GLU I 105 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.497A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET I 33 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 114 through 118 Processing sheet with id=AB7, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.405A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 423 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: 1.45 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1556 1.35 - 1.47: 1311 1.47 - 1.59: 2116 1.59 - 1.71: 0 1.71 - 1.83: 28 Bond restraints: 5011 Sorted by residual: bond pdb=" CA LYS I 24 " pdb=" C LYS I 24 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.20e-02 6.94e+03 1.39e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.20e+00 bond pdb=" CB LYS F 211 " pdb=" CG LYS F 211 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG PRO I 95 " pdb=" CD PRO I 95 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.03e+00 bond pdb=" CG LYS F 211 " pdb=" CD LYS F 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.31e-01 ... (remaining 5006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 6625 1.54 - 3.09: 151 3.09 - 4.63: 31 4.63 - 6.18: 5 6.18 - 7.72: 5 Bond angle restraints: 6817 Sorted by residual: angle pdb=" N LYS F 153 " pdb=" CA LYS F 153 " pdb=" C LYS F 153 " ideal model delta sigma weight residual 108.69 115.32 -6.63 1.77e+00 3.19e-01 1.40e+01 angle pdb=" CB LYS F 211 " pdb=" CG LYS F 211 " pdb=" CD LYS F 211 " ideal model delta sigma weight residual 111.30 119.02 -7.72 2.30e+00 1.89e-01 1.13e+01 angle pdb=" N ASP F 154 " pdb=" CA ASP F 154 " pdb=" C ASP F 154 " ideal model delta sigma weight residual 110.80 117.76 -6.96 2.13e+00 2.20e-01 1.07e+01 angle pdb=" N LEU F 151 " pdb=" CA LEU F 151 " pdb=" C LEU F 151 " ideal model delta sigma weight residual 107.75 113.39 -5.64 1.86e+00 2.89e-01 9.20e+00 angle pdb=" N ILE I 48 " pdb=" CA ILE I 48 " pdb=" C ILE I 48 " ideal model delta sigma weight residual 108.48 112.63 -4.15 1.44e+00 4.82e-01 8.31e+00 ... (remaining 6812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2691 15.79 - 31.58: 221 31.58 - 47.37: 56 47.37 - 63.15: 9 63.15 - 78.94: 4 Dihedral angle restraints: 2981 sinusoidal: 1145 harmonic: 1836 Sorted by residual: dihedral pdb=" CB CYS F 150 " pdb=" SG CYS F 150 " pdb=" SG CYS F 206 " pdb=" CB CYS F 206 " ideal model delta sinusoidal sigma weight residual -86.00 -118.96 32.96 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 65.21 27.79 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 475 0.035 - 0.070: 185 0.070 - 0.105: 65 0.105 - 0.140: 21 0.140 - 0.175: 2 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA ASP F 154 " pdb=" N ASP F 154 " pdb=" C ASP F 154 " pdb=" CB ASP F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 745 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 46 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C PHE I 46 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE I 46 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE I 47 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 46 " -0.009 2.00e-02 2.50e+03 8.91e-03 1.39e+00 pdb=" CG PHE I 46 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE I 46 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 46 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE I 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 46 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE I 46 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 14 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO I 15 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 15 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 15 " -0.016 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 392 2.75 - 3.29: 4504 3.29 - 3.82: 7513 3.82 - 4.36: 8931 4.36 - 4.90: 16163 Nonbonded interactions: 37503 Sorted by model distance: nonbonded pdb=" OG SER F 25 " pdb=" OE1 GLU F 26 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS I 18 " pdb=" OD1 ASN I 20 " model vdw 2.312 3.120 nonbonded pdb=" OG SER F 198 " pdb=" OH TYR F 204 " model vdw 2.341 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.348 3.040 nonbonded pdb=" N GLU I 79 " pdb=" OD2 ASP I 82 " model vdw 2.365 3.120 ... (remaining 37498 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: 116.400 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 : 0.003 0.032 5011 Z= 0.186 Angle : 0.633 7.723 6817 Z= 0.342 Chirality : 0.044 0.175 748 Planarity : 0.004 0.029 880 Dihedral : 12.594 78.942 1785 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.04 (0.35), residues: 625 helix: -2.16 (0.85), residues: 37 sheet: 1.28 (0.33), residues: 244 loop : -0.78 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS F 35 PHE 0.021 0.001 PHE I 46 TYR 0.013 0.001 TYR A 495 ARG 0.002 0.000 ARG I 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: F 19 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7507 (ttt180) REVERT: F 130 SER cc_start: 0.7070 (m) cc_final: 0.6704 (p) REVERT: I 42 GLU cc_start: 0.7574 (mp0) cc_final: 0.7230 (mp0) REVERT: I 122 ASP cc_start: 0.6882 (p0) cc_final: 0.6534 (p0) REVERT: I 123 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7194 (tt0) REVERT: I 170 ASP cc_start: 0.6762 (p0) cc_final: 0.6459 (p0) REVERT: I 179 LEU cc_start: 0.6648 (tp) cc_final: 0.6369 (tp) REVERT: I 199 GLN cc_start: 0.8528 (pt0) cc_final: 0.8048 (pm20) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2751 time to fit residues: 38.2626 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN I 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145215 restraints weight = 6187.925| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.49 r_work: 0.3326 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5011 Z= 0.191 Angle : 0.607 7.487 6817 Z= 0.315 Chirality : 0.045 0.142 748 Planarity : 0.004 0.040 880 Dihedral : 4.274 15.704 685 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.22 % Allowed : 7.02 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.07 (0.35), residues: 625 helix: -2.09 (0.91), residues: 32 sheet: 1.38 (0.33), residues: 245 loop : -0.95 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS F 35 PHE 0.028 0.002 PHE I 46 TYR 0.011 0.001 TYR I 140 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 19 ARG cc_start: 0.8602 (ttm170) cc_final: 0.7933 (ttt180) REVERT: F 130 SER cc_start: 0.7525 (m) cc_final: 0.7238 (p) REVERT: I 122 ASP cc_start: 0.6758 (p0) cc_final: 0.6551 (p0) REVERT: I 179 LEU cc_start: 0.6681 (tp) cc_final: 0.6475 (tp) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.2518 time to fit residues: 26.5899 Evaluate side-chains 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 0.0270 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145224 restraints weight = 6258.185| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.79 r_work: 0.3321 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5011 Z= 0.145 Angle : 0.550 6.258 6817 Z= 0.283 Chirality : 0.044 0.151 748 Planarity : 0.004 0.038 880 Dihedral : 4.060 13.952 685 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.66 % Allowed : 8.87 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.10 (0.35), residues: 625 helix: -1.90 (0.91), residues: 32 sheet: 1.44 (0.32), residues: 254 loop : -0.86 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS F 35 PHE 0.020 0.001 PHE I 46 TYR 0.011 0.001 TYR I 140 ARG 0.003 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8454 (ttp-170) REVERT: F 7 SER cc_start: 0.8478 (p) cc_final: 0.8222 (m) REVERT: F 19 ARG cc_start: 0.8508 (ttm170) cc_final: 0.7878 (ttt180) REVERT: F 130 SER cc_start: 0.7336 (m) cc_final: 0.6999 (p) REVERT: F 151 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (pp) REVERT: I 179 LEU cc_start: 0.6663 (tp) cc_final: 0.6381 (tp) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.1690 time to fit residues: 16.6336 Evaluate side-chains 74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.186807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144072 restraints weight = 6282.733| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.94 r_work: 0.3251 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5011 Z= 0.166 Angle : 0.558 5.597 6817 Z= 0.287 Chirality : 0.044 0.138 748 Planarity : 0.004 0.038 880 Dihedral : 4.069 15.854 685 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.22 % Allowed : 9.61 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.11 (0.34), residues: 625 helix: -1.98 (0.90), residues: 32 sheet: 1.34 (0.31), residues: 258 loop : -0.76 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS F 35 PHE 0.024 0.001 PHE I 46 TYR 0.012 0.001 TYR I 140 ARG 0.004 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7262 (m-30) cc_final: 0.7025 (m-30) REVERT: A 466 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8491 (ttp-170) REVERT: F 7 SER cc_start: 0.8451 (p) cc_final: 0.8123 (m) REVERT: F 19 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7878 (ttt180) REVERT: F 130 SER cc_start: 0.7252 (m) cc_final: 0.6868 (p) REVERT: F 186 TYR cc_start: 0.7208 (m-80) cc_final: 0.6958 (m-80) REVERT: I 78 ILE cc_start: 0.7829 (tt) cc_final: 0.7608 (tt) REVERT: I 122 ASP cc_start: 0.7350 (p0) cc_final: 0.6922 (p0) REVERT: I 142 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7131 (mtp85) REVERT: I 179 LEU cc_start: 0.6748 (tp) cc_final: 0.6440 (tp) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1707 time to fit residues: 17.2751 Evaluate side-chains 80 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** I 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.183403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124225 restraints weight = 6083.579| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.56 r_work: 0.3195 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5011 Z= 0.385 Angle : 0.715 9.879 6817 Z= 0.372 Chirality : 0.049 0.155 748 Planarity : 0.005 0.037 880 Dihedral : 4.813 21.576 685 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 11.28 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.05 (0.34), residues: 625 helix: -2.21 (0.82), residues: 32 sheet: 1.33 (0.32), residues: 253 loop : -0.93 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.009 0.002 HIS I 91 PHE 0.038 0.003 PHE I 46 TYR 0.022 0.002 TYR A 501 ARG 0.004 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7483 (m-30) cc_final: 0.7256 (m-30) REVERT: F 19 ARG cc_start: 0.8676 (ttm170) cc_final: 0.8044 (ttt180) REVERT: I 78 ILE cc_start: 0.8020 (tt) cc_final: 0.7723 (tt) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.1898 time to fit residues: 18.2112 Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.187990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132105 restraints weight = 6074.491| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.09 r_work: 0.3217 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5011 Z= 0.182 Angle : 0.576 6.050 6817 Z= 0.298 Chirality : 0.044 0.134 748 Planarity : 0.004 0.035 880 Dihedral : 4.330 17.574 685 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.85 % Allowed : 14.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.06 (0.34), residues: 625 helix: -2.03 (0.86), residues: 32 sheet: 1.37 (0.31), residues: 258 loop : -0.85 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS F 35 PHE 0.024 0.001 PHE I 46 TYR 0.015 0.001 TYR I 140 ARG 0.005 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: F 7 SER cc_start: 0.8569 (p) cc_final: 0.8248 (m) REVERT: F 19 ARG cc_start: 0.8626 (ttm170) cc_final: 0.8022 (ttt180) REVERT: I 78 ILE cc_start: 0.8058 (tt) cc_final: 0.7856 (tt) REVERT: I 179 LEU cc_start: 0.6302 (tp) cc_final: 0.5869 (mt) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1762 time to fit residues: 15.6105 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.184972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125424 restraints weight = 5944.618| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.95 r_work: 0.3198 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5011 Z= 0.324 Angle : 0.669 8.912 6817 Z= 0.348 Chirality : 0.047 0.153 748 Planarity : 0.004 0.034 880 Dihedral : 4.674 21.138 685 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.77 % Allowed : 14.60 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.05 (0.34), residues: 625 helix: -2.28 (0.80), residues: 32 sheet: 1.35 (0.32), residues: 264 loop : -1.02 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.008 0.001 HIS F 35 PHE 0.033 0.003 PHE I 46 TYR 0.019 0.002 TYR A 495 ARG 0.003 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 493 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8086 (mtt180) REVERT: I 78 ILE cc_start: 0.8098 (tt) cc_final: 0.7765 (tt) REVERT: I 179 LEU cc_start: 0.6507 (tp) cc_final: 0.6197 (mp) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.1968 time to fit residues: 18.0289 Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** I 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127553 restraints weight = 6095.676| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.96 r_work: 0.3296 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5011 Z= 0.199 Angle : 0.584 6.268 6817 Z= 0.302 Chirality : 0.044 0.139 748 Planarity : 0.004 0.034 880 Dihedral : 4.388 18.220 685 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.96 % Allowed : 14.60 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.04 (0.34), residues: 625 helix: -1.98 (0.87), residues: 32 sheet: 1.44 (0.32), residues: 258 loop : -0.96 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS F 35 PHE 0.023 0.002 PHE I 46 TYR 0.015 0.001 TYR I 140 ARG 0.005 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8200 (mtt180) REVERT: F 7 SER cc_start: 0.8597 (p) cc_final: 0.8294 (m) REVERT: F 130 SER cc_start: 0.7306 (m) cc_final: 0.6986 (p) REVERT: I 142 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7095 (mtp85) REVERT: I 179 LEU cc_start: 0.6275 (tp) cc_final: 0.5902 (mt) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.2330 time to fit residues: 22.8426 Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130162 restraints weight = 5997.254| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.22 r_work: 0.3176 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5011 Z= 0.315 Angle : 0.668 8.188 6817 Z= 0.347 Chirality : 0.047 0.154 748 Planarity : 0.004 0.034 880 Dihedral : 4.654 21.010 685 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.51 % Allowed : 14.23 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.03 (0.34), residues: 625 helix: -2.01 (0.88), residues: 32 sheet: 1.45 (0.33), residues: 258 loop : -1.07 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.007 0.001 HIS F 35 PHE 0.029 0.002 PHE I 46 TYR 0.020 0.002 TYR A 495 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: I 179 LEU cc_start: 0.6376 (tp) cc_final: 0.5968 (mp) outliers start: 19 outliers final: 17 residues processed: 72 average time/residue: 0.1781 time to fit residues: 16.9566 Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.184979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132142 restraints weight = 6041.114| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.02 r_work: 0.3264 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5011 Z= 0.224 Angle : 0.612 6.443 6817 Z= 0.317 Chirality : 0.045 0.141 748 Planarity : 0.004 0.037 880 Dihedral : 4.494 19.134 685 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.14 % Allowed : 14.79 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.05 (0.35), residues: 625 helix: -1.86 (0.92), residues: 32 sheet: 1.46 (0.32), residues: 264 loop : -1.04 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS F 35 PHE 0.024 0.002 PHE I 46 TYR 0.017 0.002 TYR A 495 ARG 0.008 0.001 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: I 142 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7000 (mtp85) REVERT: I 179 LEU cc_start: 0.6173 (tp) cc_final: 0.5782 (mp) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.2640 time to fit residues: 22.4302 Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4119 r_free = 0.4119 target = 0.185105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125222 restraints weight = 6112.517| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.92 r_work: 0.3189 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5011 Z= 0.216 Angle : 0.602 6.241 6817 Z= 0.312 Chirality : 0.045 0.141 748 Planarity : 0.004 0.037 880 Dihedral : 4.425 18.937 685 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.40 % Allowed : 15.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.09 (0.35), residues: 625 helix: -1.73 (0.96), residues: 32 sheet: 1.47 (0.32), residues: 265 loop : -1.02 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS F 35 PHE 0.024 0.002 PHE I 46 TYR 0.017 0.002 TYR A 495 ARG 0.002 0.000 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.31 seconds wall clock time: 72 minutes 50.40 seconds (4370.40 seconds total)