Starting phenix.real_space_refine on Thu Nov 14 00:30:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9d7k_46607/11_2024/9d7k_46607.cif" } resolution = 3.0 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= 0.022 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 13 5.16 5 C 1826 2.51 5 N 466 2.21 5 O 538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2843 Number of models: 1 Model: "" Number of chains: 1 Chain: "S" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2843 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.33, per 1000 atoms: 0.82 Number of scatterers: 2843 At special positions: 0 Unit cell: (73.44, 74.52, 66.96, 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 13 16.00 O 538 8.00 N 466 7.00 C 1826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.63 Conformation dependent library (CDL) restraints added in 349.3 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 37.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'S' and resid 48 through 68 removed outlier: 3.693A pdb=" N ALA S 52 " --> pdb=" O GLY S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 89 Processing helix chain 'S' and resid 92 through 102 removed outlier: 3.505A pdb=" N LEU S 96 " --> pdb=" O HIS S 92 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR S 97 " --> pdb=" O ASN S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 105 No H-bonds generated for 'chain 'S' and resid 103 through 105' Processing helix chain 'S' and resid 111 through 128 Processing helix chain 'S' and resid 150 through 160 Processing helix chain 'S' and resid 172 through 188 removed outlier: 3.671A pdb=" N LYS S 178 " --> pdb=" O ALA S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 226 Processing helix chain 'S' and resid 283 through 290 Processing helix chain 'S' and resid 292 through 302 removed outlier: 3.516A pdb=" N ARG S 298 " --> pdb=" O GLU S 294 " (cutoff:3.500A) Processing helix chain 'S' and resid 324 through 332 Processing helix chain 'S' and resid 334 through 338 removed outlier: 3.606A pdb=" N THR S 338 " --> pdb=" O GLU S 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 73 through 75 removed outlier: 3.563A pdb=" N PHE S 413 " --> pdb=" O ILE S 403 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS S 261 " --> pdb=" O ASP S 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE S 251 " --> pdb=" O ARG S 306 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU S 304 " --> pdb=" O TYR S 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 134 through 137 removed outlier: 3.740A pdb=" N SER S 136 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL S 206 " --> pdb=" O PHE S 142 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR S 168 " --> pdb=" O MET S 141 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL S 143 " --> pdb=" O THR S 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 134 through 137 removed outlier: 3.740A pdb=" N SER S 136 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE S 211 " --> pdb=" O LYS S 360 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE S 213 " --> pdb=" O VAL S 362 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA S 361 " --> pdb=" O ARG S 320 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG S 320 " --> pdb=" O ALA S 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 227 through 232 removed outlier: 3.628A pdb=" N SER S 229 " --> pdb=" O VAL S 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU S 311 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE S 308 " --> pdb=" O THR S 391 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL S 393 " --> pdb=" O ILE S 308 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU S 310 " --> pdb=" O VAL S 393 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 372 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: 0.79 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 917 1.34 - 1.46: 560 1.46 - 1.57: 1397 1.57 - 1.69: 0 1.69 - 1.80: 25 Bond restraints: 2899 Sorted by residual: bond pdb=" CB ASP S 321 " pdb=" CG ASP S 321 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CA ASP S 321 " pdb=" CB ASP S 321 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.55e-02 4.16e+03 7.20e-01 bond pdb=" CA GLU S 371 " pdb=" CB GLU S 371 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.61e-02 3.86e+03 5.12e-01 bond pdb=" CB PHE S 58 " pdb=" CG PHE S 58 " ideal model delta sigma weight residual 1.502 1.486 0.016 2.30e-02 1.89e+03 5.09e-01 bond pdb=" CB ASP S 70 " pdb=" CG ASP S 70 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 4.98e-01 ... (remaining 2894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 3843 1.60 - 3.20: 64 3.20 - 4.80: 13 4.80 - 6.40: 2 6.40 - 7.99: 2 Bond angle restraints: 3924 Sorted by residual: angle pdb=" C ASP S 321 " pdb=" CA ASP S 321 " pdb=" CB ASP S 321 " ideal model delta sigma weight residual 109.48 113.79 -4.31 1.68e+00 3.54e-01 6.59e+00 angle pdb=" CA ASP S 321 " pdb=" CB ASP S 321 " pdb=" CG ASP S 321 " ideal model delta sigma weight residual 112.60 114.97 -2.37 1.00e+00 1.00e+00 5.61e+00 angle pdb=" CA LEU S 133 " pdb=" CB LEU S 133 " pdb=" CG LEU S 133 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.22e+00 angle pdb=" C ALA S 349 " pdb=" N ARG S 350 " pdb=" CA ARG S 350 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.38e+00 angle pdb=" CA LEU S 195 " pdb=" CB LEU S 195 " pdb=" CG LEU S 195 " ideal model delta sigma weight residual 116.30 123.43 -7.13 3.50e+00 8.16e-02 4.15e+00 ... (remaining 3919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1495 17.15 - 34.30: 180 34.30 - 51.45: 59 51.45 - 68.60: 13 68.60 - 85.75: 5 Dihedral angle restraints: 1752 sinusoidal: 694 harmonic: 1058 Sorted by residual: dihedral pdb=" CA LYS S 101 " pdb=" C LYS S 101 " pdb=" N GLY S 102 " pdb=" CA GLY S 102 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG S 350 " pdb=" CD ARG S 350 " pdb=" NE ARG S 350 " pdb=" CZ ARG S 350 " ideal model delta sinusoidal sigma weight residual -180.00 -135.78 -44.22 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA ASN S 181 " pdb=" CB ASN S 181 " pdb=" CG ASN S 181 " pdb=" OD1 ASN S 181 " ideal model delta sinusoidal sigma weight residual -90.00 -154.79 64.79 2 2.00e+01 2.50e-03 9.82e+00 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 264 0.027 - 0.055: 120 0.055 - 0.082: 37 0.082 - 0.110: 25 0.110 - 0.137: 9 Chirality restraints: 455 Sorted by residual: chirality pdb=" CA ILE S 251 " pdb=" N ILE S 251 " pdb=" C ILE S 251 " pdb=" CB ILE S 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE S 277 " pdb=" N ILE S 277 " pdb=" C ILE S 277 " pdb=" CB ILE S 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL S 357 " pdb=" N VAL S 357 " pdb=" C VAL S 357 " pdb=" CB VAL S 357 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 452 not shown) Planarity restraints: 499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG S 397 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO S 398 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO S 398 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 398 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 404 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO S 405 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO S 405 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO S 405 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP S 321 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C ASP S 321 " 0.021 2.00e-02 2.50e+03 pdb=" O ASP S 321 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR S 322 " -0.007 2.00e-02 2.50e+03 ... (remaining 496 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 882 2.83 - 3.34: 2542 3.34 - 3.86: 4569 3.86 - 4.38: 5079 4.38 - 4.90: 8824 Nonbonded interactions: 21896 Sorted by model distance: nonbonded pdb=" ND1 HIS S 116 " pdb=" OH TYR S 161 " model vdw 2.308 3.120 nonbonded pdb=" OG SER S 317 " pdb=" OD1 ASP S 364 " model vdw 2.327 3.040 nonbonded pdb=" NE2 GLN S 117 " pdb=" OE1 GLN S 120 " model vdw 2.366 3.120 nonbonded pdb=" OG SER S 76 " pdb=" OG SER S 79 " model vdw 2.376 3.040 nonbonded pdb=" O THR S 338 " pdb=" OG1 THR S 338 " model vdw 2.416 3.040 ... (remaining 21891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.380 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.030 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 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 : 0.002 0.028 2899 Z= 0.127 Angle : 0.554 7.995 3924 Z= 0.280 Chirality : 0.042 0.137 455 Planarity : 0.004 0.040 499 Dihedral : 17.288 85.754 1060 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.60 % Allowed : 23.64 % Favored : 74.76 % 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: 0.63 (0.47), residues: 355 helix: 1.76 (0.53), residues: 115 sheet: 0.07 (0.66), residues: 81 loop : -0.32 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 299 HIS 0.003 0.001 HIS S 359 PHE 0.019 0.001 PHE S 212 TYR 0.007 0.001 TYR S 253 ARG 0.005 0.001 ARG S 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.331 Fit side-chains REVERT: S 58 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5651 (t80) REVERT: S 87 LEU cc_start: 0.7953 (tp) cc_final: 0.7667 (tm) REVERT: S 145 GLU cc_start: 0.7722 (pt0) cc_final: 0.7145 (pt0) REVERT: S 185 LYS cc_start: 0.7754 (tttt) cc_final: 0.7504 (tmtp) REVERT: S 291 LEU cc_start: 0.5915 (mt) cc_final: 0.5573 (mt) REVERT: S 333 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7202 (pt) REVERT: S 362 VAL cc_start: 0.8579 (p) cc_final: 0.8322 (p) outliers start: 5 outliers final: 1 residues processed: 122 average time/residue: 0.7325 time to fit residues: 92.7094 Evaluate side-chains 103 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 58 PHE Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 139 ASN S 186 ASN S 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2899 Z= 0.214 Angle : 0.690 8.098 3924 Z= 0.350 Chirality : 0.046 0.242 455 Planarity : 0.005 0.040 499 Dihedral : 6.083 58.780 385 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.51 % Allowed : 29.71 % Favored : 66.77 % 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: 0.82 (0.47), residues: 355 helix: 1.80 (0.51), residues: 116 sheet: 0.36 (0.59), residues: 90 loop : -0.26 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 217 HIS 0.003 0.001 HIS S 359 PHE 0.021 0.003 PHE S 212 TYR 0.015 0.002 TYR S 253 ARG 0.005 0.001 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: S 87 LEU cc_start: 0.8036 (tp) cc_final: 0.7727 (tm) REVERT: S 144 LYS cc_start: 0.7815 (tttp) cc_final: 0.7538 (tptm) REVERT: S 145 GLU cc_start: 0.7734 (pt0) cc_final: 0.7155 (pt0) REVERT: S 204 MET cc_start: 0.6715 (mmt) cc_final: 0.6467 (mmm) REVERT: S 362 VAL cc_start: 0.8403 (p) cc_final: 0.8180 (p) outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 0.9463 time to fit residues: 110.1509 Evaluate side-chains 107 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 58 PHE Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 254 PHE Chi-restraints excluded: chain S residue 402 ILE Chi-restraints excluded: chain S residue 416 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 139 ASN S 228 GLN S 330 GLN S 351 ASN S 356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2899 Z= 0.202 Angle : 0.665 7.285 3924 Z= 0.331 Chirality : 0.043 0.135 455 Planarity : 0.005 0.078 499 Dihedral : 5.163 40.496 381 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.83 % Allowed : 30.35 % Favored : 65.81 % 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: 0.69 (0.47), residues: 355 helix: 1.71 (0.50), residues: 116 sheet: 0.10 (0.60), residues: 87 loop : -0.22 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 217 HIS 0.004 0.001 HIS S 359 PHE 0.033 0.002 PHE S 75 TYR 0.014 0.002 TYR S 253 ARG 0.009 0.001 ARG S 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 87 LEU cc_start: 0.8087 (tp) cc_final: 0.7767 (tm) REVERT: S 145 GLU cc_start: 0.7718 (pt0) cc_final: 0.7086 (pt0) REVERT: S 204 MET cc_start: 0.6758 (mmt) cc_final: 0.6466 (mmm) REVERT: S 284 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6603 (tmm) REVERT: S 354 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7742 (m) REVERT: S 363 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7884 (tp) outliers start: 12 outliers final: 3 residues processed: 124 average time/residue: 0.9206 time to fit residues: 117.6508 Evaluate side-chains 118 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 139 ASN Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 416 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 GLN S 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2899 Z= 0.244 Angle : 0.727 10.921 3924 Z= 0.363 Chirality : 0.045 0.150 455 Planarity : 0.006 0.069 499 Dihedral : 4.782 19.949 379 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.88 % Allowed : 35.14 % Favored : 61.98 % 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: 0.54 (0.47), residues: 355 helix: 1.63 (0.49), residues: 116 sheet: -0.15 (0.56), residues: 94 loop : -0.22 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 217 HIS 0.003 0.001 HIS S 359 PHE 0.026 0.003 PHE S 153 TYR 0.018 0.002 TYR S 253 ARG 0.007 0.001 ARG S 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 80 ILE cc_start: 0.7968 (mm) cc_final: 0.7713 (tp) REVERT: S 87 LEU cc_start: 0.8126 (tp) cc_final: 0.7802 (tm) REVERT: S 145 GLU cc_start: 0.7676 (pt0) cc_final: 0.7012 (pt0) REVERT: S 204 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6835 (mmt) REVERT: S 240 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5476 (mtt) REVERT: S 284 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6740 (tmm) REVERT: S 399 PHE cc_start: 0.7716 (p90) cc_final: 0.7324 (p90) outliers start: 9 outliers final: 4 residues processed: 121 average time/residue: 1.0545 time to fit residues: 131.1530 Evaluate side-chains 123 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 416 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 202 GLN S 248 HIS S 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2899 Z= 0.265 Angle : 0.760 11.117 3924 Z= 0.378 Chirality : 0.045 0.158 455 Planarity : 0.005 0.060 499 Dihedral : 4.924 20.625 379 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.47 % Allowed : 36.74 % Favored : 58.79 % 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: 0.46 (0.46), residues: 355 helix: 1.54 (0.48), residues: 119 sheet: 0.04 (0.58), residues: 87 loop : -0.47 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.021 0.003 PHE S 153 TYR 0.018 0.002 TYR S 253 ARG 0.010 0.001 ARG S 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 80 ILE cc_start: 0.7959 (mm) cc_final: 0.7642 (tp) REVERT: S 84 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (mm) REVERT: S 87 LEU cc_start: 0.8127 (tp) cc_final: 0.7821 (tm) REVERT: S 145 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: S 191 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7645 (mmtt) REVERT: S 204 MET cc_start: 0.7059 (mmt) cc_final: 0.6770 (mmt) REVERT: S 240 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5504 (mtt) REVERT: S 284 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: S 350 ARG cc_start: 0.7865 (ptm160) cc_final: 0.7580 (ptp-110) REVERT: S 354 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7499 (m) REVERT: S 399 PHE cc_start: 0.7692 (p90) cc_final: 0.7420 (p90) outliers start: 14 outliers final: 4 residues processed: 123 average time/residue: 1.0199 time to fit residues: 128.9049 Evaluate side-chains 130 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 145 GLU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 416 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 GLN S 330 GLN S 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2899 Z= 0.278 Angle : 0.751 10.298 3924 Z= 0.381 Chirality : 0.046 0.172 455 Planarity : 0.006 0.063 499 Dihedral : 5.045 20.821 379 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.47 % Allowed : 35.14 % Favored : 60.38 % 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: 0.35 (0.46), residues: 355 helix: 1.63 (0.48), residues: 116 sheet: -0.23 (0.54), residues: 94 loop : -0.50 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.020 0.002 PHE S 75 TYR 0.019 0.002 TYR S 253 ARG 0.009 0.001 ARG S 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: S 80 ILE cc_start: 0.8017 (mm) cc_final: 0.7740 (tp) REVERT: S 87 LEU cc_start: 0.8143 (tp) cc_final: 0.7839 (tm) REVERT: S 145 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: S 191 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7579 (tppp) REVERT: S 200 ASP cc_start: 0.7630 (t0) cc_final: 0.7416 (t0) REVERT: S 240 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5183 (mtt) REVERT: S 284 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6205 (tmm) REVERT: S 320 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7067 (mmm-85) REVERT: S 399 PHE cc_start: 0.7738 (p90) cc_final: 0.7432 (p90) outliers start: 14 outliers final: 5 residues processed: 131 average time/residue: 0.9457 time to fit residues: 127.4961 Evaluate side-chains 131 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 145 GLU Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 290 MET Chi-restraints excluded: chain S residue 354 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 330 GLN S 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2899 Z= 0.266 Angle : 0.809 12.295 3924 Z= 0.398 Chirality : 0.046 0.173 455 Planarity : 0.006 0.066 499 Dihedral : 5.207 20.619 379 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.83 % Allowed : 38.98 % Favored : 57.19 % 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: 0.20 (0.45), residues: 355 helix: 1.59 (0.47), residues: 116 sheet: -0.39 (0.53), residues: 94 loop : -0.61 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.025 0.002 PHE S 316 TYR 0.018 0.002 TYR S 253 ARG 0.008 0.001 ARG S 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.323 Fit side-chains REVERT: S 80 ILE cc_start: 0.7976 (mm) cc_final: 0.7699 (tp) REVERT: S 87 LEU cc_start: 0.8128 (tp) cc_final: 0.7823 (tm) REVERT: S 132 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: S 145 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7032 (pt0) REVERT: S 191 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7634 (tppp) REVERT: S 204 MET cc_start: 0.6765 (mmt) cc_final: 0.6547 (mmt) REVERT: S 240 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5179 (mtt) REVERT: S 399 PHE cc_start: 0.7737 (p90) cc_final: 0.7440 (p90) outliers start: 12 outliers final: 3 residues processed: 114 average time/residue: 1.0002 time to fit residues: 117.2723 Evaluate side-chains 114 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 145 GLU Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 290 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2899 Z= 0.282 Angle : 0.818 10.846 3924 Z= 0.412 Chirality : 0.048 0.199 455 Planarity : 0.006 0.070 499 Dihedral : 5.317 20.353 379 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 38.66 % Favored : 58.15 % 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: 0.22 (0.45), residues: 355 helix: 1.45 (0.46), residues: 119 sheet: -0.12 (0.55), residues: 87 loop : -0.70 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.026 0.003 PHE S 316 TYR 0.018 0.002 TYR S 253 ARG 0.007 0.001 ARG S 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.296 Fit side-chains REVERT: S 87 LEU cc_start: 0.8134 (tp) cc_final: 0.7829 (tm) REVERT: S 132 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: S 145 GLU cc_start: 0.7579 (pt0) cc_final: 0.7047 (pt0) REVERT: S 191 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7598 (tppp) REVERT: S 240 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5257 (mtt) REVERT: S 307 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: S 399 PHE cc_start: 0.7725 (p90) cc_final: 0.7430 (p90) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 1.0040 time to fit residues: 105.3305 Evaluate side-chains 102 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 172 ASP Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 290 MET Chi-restraints excluded: chain S residue 307 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2899 Z= 0.263 Angle : 0.849 12.831 3924 Z= 0.425 Chirality : 0.048 0.195 455 Planarity : 0.006 0.073 499 Dihedral : 5.295 20.278 379 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.19 % Allowed : 39.62 % Favored : 57.19 % 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: 0.36 (0.46), residues: 355 helix: 1.64 (0.47), residues: 116 sheet: -0.24 (0.54), residues: 94 loop : -0.49 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.028 0.002 PHE S 316 TYR 0.016 0.002 TYR S 253 ARG 0.007 0.001 ARG S 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.332 Fit side-chains REVERT: S 84 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8183 (mt) REVERT: S 87 LEU cc_start: 0.8119 (tp) cc_final: 0.7815 (tm) REVERT: S 132 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: S 145 GLU cc_start: 0.7563 (pt0) cc_final: 0.7012 (pt0) REVERT: S 240 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5212 (mtt) REVERT: S 399 PHE cc_start: 0.7738 (p90) cc_final: 0.7453 (p90) outliers start: 10 outliers final: 3 residues processed: 96 average time/residue: 1.0379 time to fit residues: 102.4129 Evaluate side-chains 98 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 24 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2899 Z= 0.232 Angle : 0.838 11.529 3924 Z= 0.418 Chirality : 0.047 0.182 455 Planarity : 0.006 0.073 499 Dihedral : 5.222 19.587 379 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.60 % Allowed : 42.49 % Favored : 55.91 % 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: 0.48 (0.45), residues: 355 helix: 1.74 (0.46), residues: 117 sheet: 0.13 (0.57), residues: 87 loop : -0.67 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 238 HIS 0.005 0.001 HIS S 359 PHE 0.028 0.002 PHE S 75 TYR 0.016 0.002 TYR S 253 ARG 0.006 0.001 ARG S 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.321 Fit side-chains REVERT: S 87 LEU cc_start: 0.8105 (tp) cc_final: 0.7809 (tm) REVERT: S 132 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: S 145 GLU cc_start: 0.7598 (pt0) cc_final: 0.7022 (pt0) REVERT: S 150 LEU cc_start: 0.7464 (tp) cc_final: 0.7255 (tt) REVERT: S 204 MET cc_start: 0.6704 (mmt) cc_final: 0.6475 (mmm) REVERT: S 240 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5125 (mtt) REVERT: S 399 PHE cc_start: 0.7717 (p90) cc_final: 0.7459 (p90) outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 1.0356 time to fit residues: 106.4544 Evaluate side-chains 98 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 240 MET Chi-restraints excluded: chain S residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 139 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 = 0.4020 r_free = 0.4020 target = 0.150238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137822 restraints weight = 5005.178| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.22 r_work: 0.3748 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2899 Z= 0.282 Angle : 0.872 13.157 3924 Z= 0.435 Chirality : 0.048 0.190 455 Planarity : 0.006 0.074 499 Dihedral : 5.314 19.722 379 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.56 % Allowed : 43.13 % Favored : 54.31 % 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: 0.35 (0.45), residues: 355 helix: 1.60 (0.46), residues: 119 sheet: -0.18 (0.55), residues: 94 loop : -0.56 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 238 HIS 0.004 0.001 HIS S 359 PHE 0.040 0.003 PHE S 221 TYR 0.017 0.002 TYR S 253 ARG 0.011 0.002 ARG S 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.80 seconds wall clock time: 39 minutes 12.86 seconds (2352.86 seconds total)