Starting phenix.real_space_refine on Mon Jun 24 14:09:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/06_2024/8wll_37623_updated.pdb" } resolution = 3.74 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= 0.000 sd= 0.079 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 28 5.16 5 C 1875 2.51 5 N 433 2.21 5 O 479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2771 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 22, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.56, per 1000 atoms: 0.91 Number of scatterers: 2815 At special positions: 0 Unit cell: (73.216, 53.248, 64.064, 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 28 16.00 O 479 8.00 N 433 7.00 C 1875 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 - 3.50 Amino acid : False - 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: 1.13 Conformation dependent library (CDL) restraints added in 745.4 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 41 through 53 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 126 through 155 removed outlier: 4.112A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.942A pdb=" N ILE A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 3.822A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 245 removed outlier: 4.161A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 250 through 269 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 320 removed outlier: 3.784A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 329 through 348 Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 383 through 413 Proline residue: A 387 - end of helix removed outlier: 4.519A pdb=" N MET A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.734A pdb=" N ARG A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 446 Proline residue: A 437 - end of helix removed outlier: 4.142A pdb=" N ALA A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Proline residue: A 465 - end of helix removed outlier: 4.410A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 594 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: 0.71 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.87: 2 0.87 - 1.10: 0 1.10 - 1.34: 842 1.34 - 1.58: 1987 1.58 - 1.82: 52 Bond restraints: 2883 Sorted by residual: bond pdb=" C6 YHR A 501 " pdb=" C7 YHR A 501 " ideal model delta sigma weight residual 1.521 0.629 0.892 2.00e-02 2.50e+03 1.99e+03 bond pdb=" C13 YHR A 501 " pdb=" C14 YHR A 501 " ideal model delta sigma weight residual 1.527 0.839 0.688 2.00e-02 2.50e+03 1.18e+03 bond pdb=" C5 YHR A 501 " pdb=" C6 YHR A 501 " ideal model delta sigma weight residual 1.527 1.276 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C12 YHR A 501 " pdb=" C13 YHR A 501 " ideal model delta sigma weight residual 1.503 1.745 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C16 YHR A 501 " pdb=" C3 YHR A 501 " ideal model delta sigma weight residual 1.531 1.299 0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 2878 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 104 106.36 - 113.26: 1570 113.26 - 120.17: 1085 120.17 - 127.07: 1150 127.07 - 133.97: 34 Bond angle restraints: 3943 Sorted by residual: angle pdb=" CB MET A 397 " pdb=" CG MET A 397 " pdb=" SD MET A 397 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C7 YHR A 501 " pdb=" N8 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 111.89 122.57 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C33 YHR A 501 " pdb=" C31 YHR A 501 " pdb=" O30 YHR A 501 " ideal model delta sigma weight residual 112.77 122.76 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 118.82 -6.48 2.04e+00 2.40e-01 1.01e+01 angle pdb=" CB MET A 403 " pdb=" CG MET A 403 " pdb=" SD MET A 403 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.45e+00 ... (remaining 3938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.56: 1468 11.56 - 23.11: 147 23.11 - 34.66: 72 34.66 - 46.22: 27 46.22 - 57.77: 5 Dihedral angle restraints: 1719 sinusoidal: 619 harmonic: 1100 Sorted by residual: dihedral pdb=" CA ARG A 326 " pdb=" C ARG A 326 " pdb=" N LYS A 327 " pdb=" CA LYS A 327 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " pdb=" NE ARG A 357 " pdb=" CZ ARG A 357 " ideal model delta sinusoidal sigma weight residual 90.00 130.81 -40.81 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 1716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 483 0.348 - 0.695: 1 0.695 - 1.043: 1 1.043 - 1.391: 0 1.391 - 1.738: 1 Chirality restraints: 486 Sorted by residual: chirality pdb=" C6 YHR A 501 " pdb=" C15 YHR A 501 " pdb=" C5 YHR A 501 " pdb=" C7 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.53 0.79 1.74 2.00e-01 2.50e+01 7.55e+01 chirality pdb=" C13 YHR A 501 " pdb=" C12 YHR A 501 " pdb=" C14 YHR A 501 " pdb=" N8 YHR A 501 " both_signs ideal model delta sigma weight residual False -2.29 -1.46 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3 YHR A 501 " pdb=" C16 YHR A 501 " pdb=" C4 YHR A 501 " pdb=" O2 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.58 2.11 0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 483 not shown) Planarity restraints: 479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 291 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 292 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 250 " -0.045 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 251 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 375 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 376 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.028 5.00e-02 4.00e+02 ... (remaining 476 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 553 2.77 - 3.30: 3109 3.30 - 3.84: 4843 3.84 - 4.37: 5184 4.37 - 4.90: 9061 Nonbonded interactions: 22750 Sorted by model distance: nonbonded pdb=" C15 YHR A 501 " pdb=" N8 YHR A 501 " model vdw 2.238 2.840 nonbonded pdb=" OG SER A 137 " pdb=" OG SER A 190 " model vdw 2.268 2.440 nonbonded pdb=" O PHE A 170 " pdb=" OG1 THR A 173 " model vdw 2.281 2.440 nonbonded pdb=" O ALA A 297 " pdb=" OG SER A 300 " model vdw 2.295 2.440 nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.314 2.440 ... (remaining 22745 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 group one per residue 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: 0.560 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: 2.990 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.024 0.892 2883 Z= 1.747 Angle : 1.058 11.003 3943 Z= 0.473 Chirality : 0.102 1.738 486 Planarity : 0.007 0.083 479 Dihedral : 13.070 57.774 1017 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.44), residues: 385 helix: 0.87 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.89 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 166 TYR 0.016 0.002 TYR A 47 ARG 0.003 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.300 Fit side-chains REVERT: A 144 ILE cc_start: 0.8518 (mm) cc_final: 0.8285 (mm) REVERT: A 287 THR cc_start: 0.7984 (p) cc_final: 0.7783 (p) REVERT: A 408 TYR cc_start: 0.8277 (t80) cc_final: 0.7731 (t80) REVERT: A 453 MET cc_start: 0.7950 (mmm) cc_final: 0.7587 (mmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1051 time to fit residues: 18.7257 Evaluate side-chains 111 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2883 Z= 0.256 Angle : 0.799 9.420 3943 Z= 0.380 Chirality : 0.045 0.186 486 Planarity : 0.007 0.059 479 Dihedral : 6.957 53.825 467 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.24 % Allowed : 20.50 % Favored : 76.26 % 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: 0.86 (0.45), residues: 385 helix: 1.09 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -1.86 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 389 TYR 0.021 0.002 TYR A 341 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.301 Fit side-chains REVERT: A 402 MET cc_start: 0.8221 (mmp) cc_final: 0.7869 (mmp) REVERT: A 408 TYR cc_start: 0.8279 (t80) cc_final: 0.7931 (t80) outliers start: 9 outliers final: 4 residues processed: 135 average time/residue: 0.1067 time to fit residues: 18.0726 Evaluate side-chains 121 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2883 Z= 0.255 Angle : 0.785 7.909 3943 Z= 0.370 Chirality : 0.043 0.121 486 Planarity : 0.006 0.049 479 Dihedral : 6.318 54.144 467 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 27.70 % Favored : 69.06 % 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: 0.64 (0.44), residues: 385 helix: 1.00 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -2.78 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.001 PHE A 27 TYR 0.014 0.001 TYR A 47 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.308 Fit side-chains REVERT: A 124 LEU cc_start: 0.7574 (tt) cc_final: 0.6998 (mp) REVERT: A 230 MET cc_start: 0.8337 (ppp) cc_final: 0.8067 (tmm) REVERT: A 330 LEU cc_start: 0.7385 (mt) cc_final: 0.6777 (mt) REVERT: A 408 TYR cc_start: 0.8265 (t80) cc_final: 0.7924 (t80) REVERT: A 453 MET cc_start: 0.8254 (mmm) cc_final: 0.7858 (mmm) outliers start: 9 outliers final: 8 residues processed: 146 average time/residue: 0.1002 time to fit residues: 18.3769 Evaluate side-chains 129 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2883 Z= 0.274 Angle : 0.781 7.238 3943 Z= 0.368 Chirality : 0.044 0.197 486 Planarity : 0.005 0.041 479 Dihedral : 6.324 53.625 467 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.40 % Allowed : 26.98 % Favored : 67.63 % 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: 0.58 (0.44), residues: 385 helix: 0.99 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.99 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.020 0.002 TYR A 47 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 0.299 Fit side-chains REVERT: A 124 LEU cc_start: 0.7532 (tt) cc_final: 0.6963 (mp) REVERT: A 191 LEU cc_start: 0.8040 (tt) cc_final: 0.7744 (tt) REVERT: A 230 MET cc_start: 0.8354 (ppp) cc_final: 0.7990 (tmm) REVERT: A 330 LEU cc_start: 0.7349 (mt) cc_final: 0.6723 (mt) REVERT: A 408 TYR cc_start: 0.8249 (t80) cc_final: 0.7935 (t80) REVERT: A 453 MET cc_start: 0.8280 (mmm) cc_final: 0.7906 (mmm) outliers start: 15 outliers final: 13 residues processed: 147 average time/residue: 0.1010 time to fit residues: 18.9184 Evaluate side-chains 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2883 Z= 0.272 Angle : 0.816 12.475 3943 Z= 0.380 Chirality : 0.045 0.187 486 Planarity : 0.005 0.041 479 Dihedral : 6.136 53.279 467 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.40 % Allowed : 30.94 % Favored : 63.67 % 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: 0.56 (0.44), residues: 385 helix: 1.03 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -3.01 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.014 0.002 TYR A 47 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.356 Fit side-chains REVERT: A 191 LEU cc_start: 0.8124 (tt) cc_final: 0.7827 (tt) REVERT: A 315 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 408 TYR cc_start: 0.8193 (t80) cc_final: 0.7932 (t80) REVERT: A 453 MET cc_start: 0.8261 (mmm) cc_final: 0.7910 (mmm) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1078 time to fit residues: 17.2581 Evaluate side-chains 131 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0370 chunk 36 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2883 Z= 0.242 Angle : 0.820 10.329 3943 Z= 0.380 Chirality : 0.044 0.175 486 Planarity : 0.005 0.041 479 Dihedral : 5.992 52.715 467 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.60 % Allowed : 33.09 % Favored : 63.31 % 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: 0.57 (0.44), residues: 385 helix: 1.01 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.86 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.021 0.001 PHE A 389 TYR 0.017 0.002 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.376 Fit side-chains REVERT: A 133 LEU cc_start: 0.8394 (mm) cc_final: 0.7828 (tp) REVERT: A 191 LEU cc_start: 0.8075 (tt) cc_final: 0.7778 (tt) REVERT: A 341 TYR cc_start: 0.8117 (t80) cc_final: 0.7858 (t80) REVERT: A 408 TYR cc_start: 0.8190 (t80) cc_final: 0.7935 (t80) REVERT: A 453 MET cc_start: 0.8251 (mmm) cc_final: 0.7968 (mmm) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.0995 time to fit residues: 18.1168 Evaluate side-chains 127 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2883 Z= 0.259 Angle : 0.866 12.935 3943 Z= 0.397 Chirality : 0.045 0.187 486 Planarity : 0.005 0.039 479 Dihedral : 5.897 51.371 467 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.24 % Allowed : 33.81 % Favored : 62.95 % 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: 0.52 (0.44), residues: 385 helix: 0.97 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.79 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 27 TYR 0.015 0.002 TYR A 47 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.325 Fit side-chains REVERT: A 175 MET cc_start: 0.7580 (mtp) cc_final: 0.7233 (mtp) REVERT: A 191 LEU cc_start: 0.8131 (tt) cc_final: 0.7833 (tt) REVERT: A 408 TYR cc_start: 0.8194 (t80) cc_final: 0.7955 (t80) REVERT: A 453 MET cc_start: 0.8292 (mmm) cc_final: 0.7974 (mmm) outliers start: 9 outliers final: 9 residues processed: 129 average time/residue: 0.1148 time to fit residues: 19.0747 Evaluate side-chains 130 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2883 Z= 0.261 Angle : 0.855 11.258 3943 Z= 0.397 Chirality : 0.046 0.212 486 Planarity : 0.005 0.039 479 Dihedral : 5.979 52.621 467 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.40 % Allowed : 32.73 % Favored : 61.87 % 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: 0.49 (0.44), residues: 385 helix: 0.94 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.78 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.002 0.001 HIS A 353 PHE 0.020 0.001 PHE A 389 TYR 0.019 0.002 TYR A 47 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.323 Fit side-chains REVERT: A 175 MET cc_start: 0.7608 (mtp) cc_final: 0.7261 (mtp) REVERT: A 191 LEU cc_start: 0.8127 (tt) cc_final: 0.7822 (tt) REVERT: A 210 VAL cc_start: 0.8098 (t) cc_final: 0.7872 (t) REVERT: A 408 TYR cc_start: 0.8184 (t80) cc_final: 0.7951 (t80) REVERT: A 453 MET cc_start: 0.8318 (mmm) cc_final: 0.8004 (mmm) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.1125 time to fit residues: 18.3685 Evaluate side-chains 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2883 Z= 0.277 Angle : 0.878 13.497 3943 Z= 0.409 Chirality : 0.047 0.192 486 Planarity : 0.005 0.039 479 Dihedral : 6.028 53.197 467 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.40 % Allowed : 32.73 % Favored : 61.87 % 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: 0.44 (0.44), residues: 385 helix: 0.94 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.90 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 27 TYR 0.015 0.002 TYR A 47 ARG 0.004 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.273 Fit side-chains REVERT: A 175 MET cc_start: 0.7637 (mtp) cc_final: 0.7286 (mtp) REVERT: A 191 LEU cc_start: 0.8082 (tt) cc_final: 0.7773 (tt) REVERT: A 408 TYR cc_start: 0.8178 (t80) cc_final: 0.7956 (t80) REVERT: A 453 MET cc_start: 0.8343 (mmm) cc_final: 0.8017 (mmm) outliers start: 15 outliers final: 13 residues processed: 129 average time/residue: 0.1019 time to fit residues: 16.6106 Evaluate side-chains 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0870 chunk 32 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2883 Z= 0.265 Angle : 0.879 12.614 3943 Z= 0.409 Chirality : 0.047 0.192 486 Planarity : 0.005 0.039 479 Dihedral : 6.116 53.244 467 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.88 % Allowed : 36.33 % Favored : 60.79 % 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: 0.41 (0.44), residues: 385 helix: 0.89 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.96 (0.78), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS A 53 PHE 0.023 0.001 PHE A 303 TYR 0.014 0.002 TYR A 341 ARG 0.004 0.001 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.316 Fit side-chains REVERT: A 124 LEU cc_start: 0.7502 (tt) cc_final: 0.7114 (mt) REVERT: A 133 LEU cc_start: 0.8435 (mm) cc_final: 0.8081 (mm) REVERT: A 152 LEU cc_start: 0.8952 (tp) cc_final: 0.8712 (tt) REVERT: A 175 MET cc_start: 0.7596 (mtp) cc_final: 0.7249 (mtp) REVERT: A 191 LEU cc_start: 0.7965 (tt) cc_final: 0.7646 (tt) REVERT: A 230 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7834 (tmm) REVERT: A 327 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7691 (mtmm) REVERT: A 330 LEU cc_start: 0.7232 (mt) cc_final: 0.6808 (mt) REVERT: A 408 TYR cc_start: 0.8171 (t80) cc_final: 0.7918 (t80) REVERT: A 453 MET cc_start: 0.8280 (mmm) cc_final: 0.7999 (mmm) outliers start: 8 outliers final: 7 residues processed: 140 average time/residue: 0.1039 time to fit residues: 18.4377 Evaluate side-chains 130 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 0 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128440 restraints weight = 5274.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131977 restraints weight = 3052.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134529 restraints weight = 1998.918| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2883 Z= 0.279 Angle : 0.946 15.421 3943 Z= 0.431 Chirality : 0.050 0.297 486 Planarity : 0.005 0.039 479 Dihedral : 6.397 59.160 467 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.88 % Allowed : 39.21 % Favored : 57.91 % 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: 0.25 (0.44), residues: 385 helix: 0.80 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.07 (0.75), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.013 0.004 HIS A 53 PHE 0.024 0.001 PHE A 303 TYR 0.022 0.002 TYR A 341 ARG 0.004 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.44 seconds wall clock time: 20 minutes 30.13 seconds (1230.13 seconds total)