Starting phenix.real_space_refine on Fri Aug 2 13:55:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlk_37622/08_2024/8wlk_37622.cif" } resolution = 3.37 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= 0.094 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 24 5.16 5 C 1918 2.51 5 N 445 2.21 5 O 486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2873 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2850 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.91 Number of scatterers: 2873 At special positions: 0 Unit cell: (58.716, 74.56, 69.9, 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 24 16.00 O 486 8.00 N 445 7.00 C 1918 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: 1.15 Conformation dependent library (CDL) restraints added in 696.3 milliseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.601A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 128 through 157 removed outlier: 4.610A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.400A 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: 3.924A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.817A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.670A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 5.456A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.954A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.876A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 4.182A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 238 hydrogen bonds defined for protein. 690 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: 0.77 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 434 1.31 - 1.44: 761 1.44 - 1.56: 1705 1.56 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 2943 Sorted by residual: bond pdb=" C05 EBZ A 501 " pdb=" N04 EBZ A 501 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C06 EBZ A 501 " pdb=" C07 EBZ A 501 " ideal model delta sigma weight residual 1.392 1.317 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C12 EBZ A 501 " pdb=" C14 EBZ A 501 " ideal model delta sigma weight residual 1.525 1.592 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C12 EBZ A 501 " pdb=" N04 EBZ A 501 " ideal model delta sigma weight residual 1.452 1.391 0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C07 EBZ A 501 " pdb=" C14 EBZ A 501 " ideal model delta sigma weight residual 1.512 1.570 -0.058 2.00e-02 2.50e+03 8.51e+00 ... (remaining 2938 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 113 106.25 - 113.18: 1574 113.18 - 120.11: 1079 120.11 - 127.04: 1213 127.04 - 133.97: 32 Bond angle restraints: 4011 Sorted by residual: angle pdb=" N ASN A 146 " pdb=" CA ASN A 146 " pdb=" C ASN A 146 " ideal model delta sigma weight residual 109.81 116.67 -6.86 2.21e+00 2.05e-01 9.62e+00 angle pdb=" CA LEU A 152 " pdb=" CB LEU A 152 " pdb=" CG LEU A 152 " ideal model delta sigma weight residual 116.30 126.76 -10.46 3.50e+00 8.16e-02 8.93e+00 angle pdb=" C06 EBZ A 501 " pdb=" C05 EBZ A 501 " pdb=" C08 EBZ A 501 " ideal model delta sigma weight residual 115.53 106.85 8.68 3.00e+00 1.11e-01 8.37e+00 angle pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" CD PRO A 45 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.22e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.12 -6.31 2.21e+00 2.05e-01 8.14e+00 ... (remaining 4006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 1671 28.64 - 57.28: 58 57.28 - 85.91: 8 85.91 - 114.55: 3 114.55 - 143.19: 1 Dihedral angle restraints: 1741 sinusoidal: 658 harmonic: 1083 Sorted by residual: dihedral pdb=" C13 EBZ A 501 " pdb=" C18 EBZ A 501 " pdb=" C19 EBZ A 501 " pdb=" C23 EBZ A 501 " ideal model delta sinusoidal sigma weight residual 59.15 -157.66 -143.19 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C13 EBZ A 501 " pdb=" C18 EBZ A 501 " pdb=" C19 EBZ A 501 " pdb=" C22 EBZ A 501 " ideal model delta sinusoidal sigma weight residual 182.76 79.21 103.55 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA ILE A 395 " pdb=" C ILE A 395 " pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 325 0.044 - 0.087: 113 0.087 - 0.131: 35 0.131 - 0.174: 6 0.174 - 0.217: 2 Chirality restraints: 481 Sorted by residual: chirality pdb=" C05 EBZ A 501 " pdb=" C06 EBZ A 501 " pdb=" C08 EBZ A 501 " pdb=" N04 EBZ A 501 " both_signs ideal model delta sigma weight residual False 2.38 2.16 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 427 " pdb=" CA VAL A 427 " pdb=" CG1 VAL A 427 " pdb=" CG2 VAL A 427 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE A 317 " pdb=" N ILE A 317 " pdb=" C ILE A 317 " pdb=" CB ILE A 317 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 478 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 44 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A 45 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 468 " -0.010 2.00e-02 2.50e+03 1.62e-02 4.57e+00 pdb=" CG PHE A 468 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 468 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 468 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 468 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 468 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 468 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " -0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 161 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.023 5.00e-02 4.00e+02 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 506 2.76 - 3.30: 3017 3.30 - 3.83: 4935 3.83 - 4.37: 5411 4.37 - 4.90: 9537 Nonbonded interactions: 23406 Sorted by model distance: nonbonded pdb=" NE2 GLN A 142 " pdb=" OD2 ASP A 426 " model vdw 2.227 3.120 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 179 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A 194 " pdb=" OG SER A 197 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 273 " pdb=" NH1 ARG A 274 " model vdw 2.346 3.120 nonbonded pdb=" OH TYR A 341 " pdb=" OD2 ASP A 399 " model vdw 2.381 3.040 ... (remaining 23401 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: 0.650 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: 0.020 Set scattering table: 0.030 Process input model: 13.450 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 : 0.006 0.075 2943 Z= 0.367 Angle : 0.907 10.461 4011 Z= 0.424 Chirality : 0.049 0.217 481 Planarity : 0.007 0.107 492 Dihedral : 15.662 143.186 1051 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.01 (0.43), residues: 379 helix: 0.53 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.036 0.002 PHE A 468 TYR 0.008 0.001 TYR A 422 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.289 Fit side-chains REVERT: A 291 ASP cc_start: 0.8884 (t70) cc_final: 0.8383 (t0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1063 time to fit residues: 13.8608 Evaluate side-chains 92 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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: 0.7170 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2943 Z= 0.207 Angle : 0.703 7.374 4011 Z= 0.343 Chirality : 0.043 0.175 481 Planarity : 0.006 0.068 492 Dihedral : 11.335 140.734 435 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.66 % Allowed : 17.28 % Favored : 80.07 % 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 (0.44), residues: 379 helix: 0.87 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.55 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.020 0.002 PHE A 468 TYR 0.011 0.001 TYR A 341 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.314 Fit side-chains REVERT: A 453 MET cc_start: 0.6794 (mmp) cc_final: 0.6157 (mmp) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.1043 time to fit residues: 12.7281 Evaluate side-chains 92 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2943 Z= 0.200 Angle : 0.659 6.309 4011 Z= 0.327 Chirality : 0.042 0.157 481 Planarity : 0.005 0.055 492 Dihedral : 10.817 133.689 435 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.98 % Allowed : 21.59 % Favored : 73.42 % 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: 0.76 (0.44), residues: 379 helix: 1.09 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.52 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.014 0.001 PHE A 429 TYR 0.009 0.001 TYR A 341 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.323 Fit side-chains REVERT: A 152 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7060 (mp) REVERT: A 308 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5330 (mm) REVERT: A 341 TYR cc_start: 0.8221 (t80) cc_final: 0.7969 (t80) REVERT: A 347 ILE cc_start: 0.7259 (tp) cc_final: 0.6957 (tp) REVERT: A 397 MET cc_start: 0.7439 (mmt) cc_final: 0.7061 (mmp) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.0921 time to fit residues: 12.0347 Evaluate side-chains 98 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2943 Z= 0.245 Angle : 0.648 6.992 4011 Z= 0.324 Chirality : 0.043 0.129 481 Planarity : 0.005 0.048 492 Dihedral : 10.551 125.753 435 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.32 % Allowed : 24.58 % Favored : 71.10 % 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: 0.98 (0.44), residues: 379 helix: 1.26 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.49 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.017 0.002 PHE A 429 TYR 0.014 0.001 TYR A 341 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.312 Fit side-chains REVERT: A 152 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7175 (mp) REVERT: A 308 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5751 (mm) REVERT: A 347 ILE cc_start: 0.7281 (tp) cc_final: 0.7032 (tp) REVERT: A 453 MET cc_start: 0.7568 (mmm) cc_final: 0.7232 (mmp) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.0949 time to fit residues: 12.6688 Evaluate side-chains 101 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2943 Z= 0.254 Angle : 0.676 6.817 4011 Z= 0.336 Chirality : 0.043 0.130 481 Planarity : 0.005 0.045 492 Dihedral : 10.558 124.250 435 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 6.31 % Allowed : 24.25 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.43), residues: 379 helix: 1.27 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.47 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.004 0.002 HIS A 353 PHE 0.014 0.001 PHE A 429 TYR 0.010 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.296 Fit side-chains REVERT: A 152 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7218 (mp) REVERT: A 271 GLN cc_start: 0.7376 (tt0) cc_final: 0.7095 (tt0) REVERT: A 308 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6292 (mm) REVERT: A 347 ILE cc_start: 0.7350 (tp) cc_final: 0.7095 (tp) REVERT: A 449 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6846 (t80) REVERT: A 453 MET cc_start: 0.7752 (mmm) cc_final: 0.7336 (mmp) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.0924 time to fit residues: 13.3107 Evaluate side-chains 108 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2943 Z= 0.232 Angle : 0.681 6.741 4011 Z= 0.340 Chirality : 0.044 0.196 481 Planarity : 0.005 0.041 492 Dihedral : 10.393 125.883 435 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.65 % Allowed : 24.92 % Favored : 69.44 % 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: 0.97 (0.43), residues: 379 helix: 1.24 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.48 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.003 0.002 HIS A 353 PHE 0.015 0.001 PHE A 429 TYR 0.009 0.001 TYR A 341 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.307 Fit side-chains REVERT: A 152 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7412 (tp) REVERT: A 271 GLN cc_start: 0.7349 (tt0) cc_final: 0.7058 (tt0) REVERT: A 295 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 347 ILE cc_start: 0.7441 (tp) cc_final: 0.7191 (tp) REVERT: A 426 ASP cc_start: 0.7725 (t70) cc_final: 0.7371 (t70) REVERT: A 449 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 453 MET cc_start: 0.7760 (mmm) cc_final: 0.7322 (mmp) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.1013 time to fit residues: 13.5945 Evaluate side-chains 107 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7280 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2943 Z= 0.224 Angle : 0.697 7.904 4011 Z= 0.342 Chirality : 0.043 0.193 481 Planarity : 0.005 0.040 492 Dihedral : 10.316 127.234 435 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.65 % Allowed : 26.25 % Favored : 68.11 % 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: 0.96 (0.43), residues: 379 helix: 1.23 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -1.45 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.013 0.001 PHE A 27 TYR 0.009 0.001 TYR A 422 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.315 Fit side-chains REVERT: A 152 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 221 MET cc_start: 0.7986 (mmm) cc_final: 0.7506 (mtp) REVERT: A 271 GLN cc_start: 0.7271 (tt0) cc_final: 0.6943 (tt0) REVERT: A 295 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (mm) REVERT: A 347 ILE cc_start: 0.7373 (tp) cc_final: 0.7119 (tp) REVERT: A 426 ASP cc_start: 0.7755 (t70) cc_final: 0.7327 (t70) REVERT: A 449 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 453 MET cc_start: 0.7748 (mmm) cc_final: 0.7285 (mmp) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.0926 time to fit residues: 12.3098 Evaluate side-chains 106 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2943 Z= 0.218 Angle : 0.676 8.094 4011 Z= 0.334 Chirality : 0.042 0.189 481 Planarity : 0.005 0.040 492 Dihedral : 10.231 127.723 435 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.31 % Allowed : 26.25 % Favored : 67.44 % 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: 0.90 (0.43), residues: 379 helix: 1.18 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -1.43 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.001 PHE A 27 TYR 0.009 0.001 TYR A 422 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.311 Fit side-chains REVERT: A 152 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7336 (tp) REVERT: A 221 MET cc_start: 0.7904 (mmm) cc_final: 0.7520 (mtp) REVERT: A 295 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 347 ILE cc_start: 0.7330 (tp) cc_final: 0.7077 (tp) REVERT: A 426 ASP cc_start: 0.7767 (t70) cc_final: 0.7360 (t70) REVERT: A 449 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 453 MET cc_start: 0.7740 (mmm) cc_final: 0.7271 (mmp) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.1000 time to fit residues: 13.2064 Evaluate side-chains 106 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2943 Z= 0.226 Angle : 0.694 8.138 4011 Z= 0.338 Chirality : 0.043 0.191 481 Planarity : 0.005 0.040 492 Dihedral : 10.230 128.071 435 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.65 % Allowed : 26.91 % Favored : 67.44 % 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: 0.87 (0.43), residues: 379 helix: 1.17 (0.29), residues: 296 sheet: None (None), residues: 0 loop : -1.46 (0.71), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 135 TYR 0.012 0.001 TYR A 422 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.312 Fit side-chains REVERT: A 152 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7357 (tp) REVERT: A 221 MET cc_start: 0.7899 (mmm) cc_final: 0.7595 (mtp) REVERT: A 271 GLN cc_start: 0.7343 (tt0) cc_final: 0.7051 (tt0) REVERT: A 295 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 347 ILE cc_start: 0.7352 (tp) cc_final: 0.7072 (tp) REVERT: A 426 ASP cc_start: 0.7764 (t70) cc_final: 0.7387 (t70) REVERT: A 453 MET cc_start: 0.7729 (mmm) cc_final: 0.7312 (mmp) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 0.0906 time to fit residues: 12.0821 Evaluate side-chains 105 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2943 Z= 0.220 Angle : 0.699 8.371 4011 Z= 0.340 Chirality : 0.043 0.185 481 Planarity : 0.005 0.040 492 Dihedral : 10.191 128.018 435 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.64 % Allowed : 25.58 % Favored : 67.77 % 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: 0.90 (0.43), residues: 379 helix: 1.21 (0.29), residues: 295 sheet: None (None), residues: 0 loop : -1.52 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.014 0.001 PHE A 27 TYR 0.015 0.001 TYR A 422 ARG 0.003 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.307 Fit side-chains REVERT: A 221 MET cc_start: 0.7803 (mmm) cc_final: 0.7588 (mtp) REVERT: A 271 GLN cc_start: 0.7331 (tt0) cc_final: 0.7050 (tt0) REVERT: A 295 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8155 (mm) REVERT: A 347 ILE cc_start: 0.7298 (tp) cc_final: 0.7036 (tp) REVERT: A 426 ASP cc_start: 0.7776 (t70) cc_final: 0.7412 (t70) REVERT: A 453 MET cc_start: 0.7761 (mmm) cc_final: 0.7347 (mmp) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.0957 time to fit residues: 13.0790 Evaluate side-chains 105 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155530 restraints weight = 4236.248| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.21 r_work: 0.3733 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2943 Z= 0.218 Angle : 0.708 8.294 4011 Z= 0.344 Chirality : 0.043 0.182 481 Planarity : 0.005 0.040 492 Dihedral : 10.190 128.401 435 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.98 % Allowed : 26.91 % Favored : 68.11 % 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 (0.43), residues: 379 helix: 1.15 (0.29), residues: 295 sheet: None (None), residues: 0 loop : -1.53 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.001 PHE A 27 TYR 0.018 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.57 seconds wall clock time: 18 minutes 54.84 seconds (1134.84 seconds total)