Starting phenix.real_space_refine on Wed Jan 17 14:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/01_2024/7zha_14728_updated.pdb" } resolution = 3.55 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2543 2.51 5 N 632 2.21 5 O 639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3836 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3836 Unusual residues: {'JDW': 1} Classifications: {'peptide': 487, 'undetermined': 1} Link IDs: {'PTRANS': 23, 'TRANS': 463, None: 1} Not linked: pdbres="LEU A 535 " pdbres="JDW A 601 " Chain breaks: 3 Time building chain proxies: 2.59, per 1000 atoms: 0.68 Number of scatterers: 3836 At special positions: 0 Unit cell: (98.34, 64.02, 81.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 639 8.00 N 632 7.00 C 2543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 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: 1.89 Conformation dependent library (CDL) restraints added in 671.7 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 1 sheets defined 71.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 16 through 41 removed outlier: 4.722A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.508A pdb=" N THR A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 205 through 233 removed outlier: 3.976A pdb=" N PHE A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 263 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 267 through 282 Proline residue: A 277 - end of helix removed outlier: 3.932A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 345 through 372 removed outlier: 3.942A pdb=" N MET A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.842A pdb=" N LEU A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 469 through 494 Proline residue: A 485 - end of helix removed outlier: 3.914A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 4.005A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.582A pdb=" N LYS A 534 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 237 hydrogen bonds defined for protein. 636 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: 0.99 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1174 1.34 - 1.46: 782 1.46 - 1.58: 1947 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 3933 Sorted by residual: bond pdb=" C11 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.337 1.435 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C13 JDW A 601 " pdb=" N2 JDW A 601 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C3 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.382 1.451 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N ASP A 5 " pdb=" CA ASP A 5 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.76e+00 bond pdb=" C7 JDW A 601 " pdb=" C8 JDW A 601 " ideal model delta sigma weight residual 1.411 1.359 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 3928 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.42: 84 105.42 - 112.57: 2023 112.57 - 119.71: 1272 119.71 - 126.85: 1913 126.85 - 134.00: 61 Bond angle restraints: 5353 Sorted by residual: angle pdb=" CA MET A 248 " pdb=" CB MET A 248 " pdb=" CG MET A 248 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA ASP A 5 " pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 121.07 118.19 2.88 1.10e+00 8.26e-01 6.84e+00 angle pdb=" C TRP A 152 " pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta sigma weight residual 121.18 116.03 5.15 1.98e+00 2.55e-01 6.77e+00 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 111.91 109.63 2.28 8.90e-01 1.26e+00 6.57e+00 angle pdb=" CA THR A 528 " pdb=" CB THR A 528 " pdb=" CG2 THR A 528 " ideal model delta sigma weight residual 110.50 114.77 -4.27 1.70e+00 3.46e-01 6.31e+00 ... (remaining 5348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1997 15.84 - 31.69: 203 31.69 - 47.53: 57 47.53 - 63.37: 9 63.37 - 79.22: 5 Dihedral angle restraints: 2271 sinusoidal: 892 harmonic: 1379 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 127 " pdb=" CB CYS A 127 " ideal model delta sinusoidal sigma weight residual 93.00 43.38 49.62 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -125.09 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA ASN A 467 " pdb=" C ASN A 467 " pdb=" N PHE A 468 " pdb=" CA PHE A 468 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 534 0.060 - 0.119: 75 0.119 - 0.179: 9 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 619 Sorted by residual: chirality pdb=" CG LEU A 124 " pdb=" CB LEU A 124 " pdb=" CD1 LEU A 124 " pdb=" CD2 LEU A 124 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA MET A 153 " pdb=" N MET A 153 " pdb=" C MET A 153 " pdb=" CB MET A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB THR A 528 " pdb=" CA THR A 528 " pdb=" OG1 THR A 528 " pdb=" CG2 THR A 528 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 616 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 292 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.008 2.00e-02 2.50e+03 1.37e-02 3.77e+00 pdb=" CG TYR A 284 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 34 " -0.010 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE A 34 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 34 " -0.000 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1352 2.86 - 3.37: 4281 3.37 - 3.88: 6382 3.88 - 4.39: 6978 4.39 - 4.90: 11474 Nonbonded interactions: 30467 Sorted by model distance: nonbonded pdb=" O ARG A 343 " pdb=" OG1 THR A 344 " model vdw 2.352 2.440 nonbonded pdb=" NH1 ARG A 407 " pdb=" O LEU A 517 " model vdw 2.362 2.520 nonbonded pdb=" O LEU A 154 " pdb=" OG1 THR A 157 " model vdw 2.370 2.440 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.380 2.440 nonbonded pdb=" NE2 GLN A 18 " pdb=" O ILE A 233 " model vdw 2.395 2.520 ... (remaining 30462 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.520 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 3933 Z= 0.324 Angle : 0.734 7.522 5353 Z= 0.377 Chirality : 0.044 0.299 619 Planarity : 0.005 0.076 660 Dihedral : 14.090 79.215 1383 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.50 % Allowed : 0.99 % Favored : 98.51 % 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: 1.39 (0.39), residues: 479 helix: 1.52 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.62 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.028 0.002 PHE A 34 TYR 0.031 0.002 TYR A 284 ARG 0.005 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 3 SER cc_start: 0.5832 (OUTLIER) cc_final: 0.4118 (p) REVERT: A 281 PHE cc_start: 0.8611 (m-10) cc_final: 0.8374 (m-80) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1288 time to fit residues: 15.9767 Evaluate side-chains 75 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 335 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3933 Z= 0.177 Angle : 0.631 7.715 5353 Z= 0.318 Chirality : 0.040 0.196 619 Planarity : 0.005 0.053 660 Dihedral : 4.827 46.970 537 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.23 % Allowed : 12.66 % Favored : 84.12 % 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: 1.55 (0.39), residues: 479 helix: 1.63 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -0.55 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 71 HIS 0.005 0.002 HIS A 48 PHE 0.024 0.002 PHE A 34 TYR 0.011 0.001 TYR A 284 ARG 0.003 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.6012 (OUTLIER) cc_final: 0.4170 (p) REVERT: A 87 ARG cc_start: 0.6669 (mtp85) cc_final: 0.6441 (mtp85) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.1238 time to fit residues: 13.4762 Evaluate side-chains 75 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3933 Z= 0.192 Angle : 0.621 9.424 5353 Z= 0.310 Chirality : 0.039 0.162 619 Planarity : 0.004 0.043 660 Dihedral : 4.193 21.768 537 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.47 % Allowed : 16.87 % Favored : 79.65 % 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: 1.45 (0.39), residues: 479 helix: 1.59 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -0.76 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 71 HIS 0.003 0.002 HIS A 48 PHE 0.023 0.002 PHE A 356 TYR 0.012 0.001 TYR A 284 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 162 ASN cc_start: 0.8993 (t0) cc_final: 0.8732 (t0) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1156 time to fit residues: 12.9917 Evaluate side-chains 79 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.0170 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3933 Z= 0.189 Angle : 0.614 11.471 5353 Z= 0.305 Chirality : 0.038 0.141 619 Planarity : 0.004 0.037 660 Dihedral : 4.155 19.860 536 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.47 % Allowed : 18.11 % Favored : 77.42 % 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: 1.50 (0.39), residues: 479 helix: 1.64 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.73 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.018 0.002 PHE A 34 TYR 0.017 0.001 TYR A 284 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5858 (OUTLIER) cc_final: 0.5305 (m-10) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.1420 time to fit residues: 14.4992 Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.0270 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3933 Z= 0.179 Angle : 0.611 12.960 5353 Z= 0.303 Chirality : 0.038 0.130 619 Planarity : 0.004 0.035 660 Dihedral : 4.087 18.374 536 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.97 % Allowed : 20.84 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.39), residues: 479 helix: 1.66 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.73 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 71 HIS 0.005 0.002 HIS A 48 PHE 0.022 0.001 PHE A 34 TYR 0.015 0.001 TYR A 284 ARG 0.006 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5846 (OUTLIER) cc_final: 0.5295 (m-10) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.1280 time to fit residues: 14.1004 Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3933 Z= 0.205 Angle : 0.645 12.835 5353 Z= 0.321 Chirality : 0.039 0.133 619 Planarity : 0.004 0.035 660 Dihedral : 4.137 18.095 536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.71 % Allowed : 21.09 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.40), residues: 479 helix: 1.63 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.74 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 71 HIS 0.005 0.002 HIS A 48 PHE 0.024 0.002 PHE A 34 TYR 0.036 0.002 TYR A 284 ARG 0.006 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5885 (OUTLIER) cc_final: 0.5311 (m-10) REVERT: A 185 TYR cc_start: 0.7572 (t80) cc_final: 0.7258 (t80) outliers start: 19 outliers final: 15 residues processed: 75 average time/residue: 0.1372 time to fit residues: 13.5018 Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3933 Z= 0.188 Angle : 0.643 13.994 5353 Z= 0.318 Chirality : 0.038 0.126 619 Planarity : 0.004 0.035 660 Dihedral : 4.148 19.030 536 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.96 % Allowed : 21.34 % Favored : 73.70 % 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: 1.52 (0.40), residues: 479 helix: 1.69 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.75 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 71 HIS 0.010 0.004 HIS A 48 PHE 0.025 0.002 PHE A 34 TYR 0.028 0.002 TYR A 284 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5850 (OUTLIER) cc_final: 0.5288 (m-10) outliers start: 20 outliers final: 16 residues processed: 88 average time/residue: 0.1447 time to fit residues: 16.1273 Evaluate side-chains 84 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3933 Z= 0.223 Angle : 0.670 13.523 5353 Z= 0.330 Chirality : 0.039 0.133 619 Planarity : 0.004 0.036 660 Dihedral : 4.238 19.488 536 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.21 % Allowed : 22.08 % Favored : 72.70 % 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: 1.39 (0.40), residues: 479 helix: 1.56 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.63 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 71 HIS 0.005 0.002 HIS A 48 PHE 0.025 0.002 PHE A 34 TYR 0.030 0.002 TYR A 284 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5919 (OUTLIER) cc_final: 0.5315 (m-10) REVERT: A 185 TYR cc_start: 0.7548 (t80) cc_final: 0.7220 (t80) outliers start: 21 outliers final: 19 residues processed: 80 average time/residue: 0.1417 time to fit residues: 14.6042 Evaluate side-chains 82 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.0040 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3933 Z= 0.175 Angle : 0.663 14.851 5353 Z= 0.323 Chirality : 0.038 0.139 619 Planarity : 0.004 0.037 660 Dihedral : 4.088 18.511 536 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.38 % Favored : 95.41 % Rotamer: Outliers : 3.97 % Allowed : 23.82 % Favored : 72.21 % 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: 1.36 (0.40), residues: 479 helix: 1.57 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -0.80 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 PHE 0.029 0.002 PHE A 34 TYR 0.025 0.001 TYR A 284 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 281 PHE cc_start: 0.8329 (m-80) cc_final: 0.7904 (m-80) outliers start: 16 outliers final: 15 residues processed: 85 average time/residue: 0.1326 time to fit residues: 14.7265 Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0070 chunk 38 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3933 Z= 0.173 Angle : 0.633 14.373 5353 Z= 0.312 Chirality : 0.038 0.126 619 Planarity : 0.004 0.037 660 Dihedral : 3.972 16.387 536 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer: Outliers : 3.72 % Allowed : 25.56 % Favored : 70.72 % 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: 1.43 (0.40), residues: 479 helix: 1.68 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.81 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 71 HIS 0.002 0.001 HIS A 48 PHE 0.028 0.001 PHE A 34 TYR 0.024 0.001 TYR A 284 ARG 0.002 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.7520 (t80) cc_final: 0.7212 (t80) REVERT: A 281 PHE cc_start: 0.8469 (m-80) cc_final: 0.7981 (m-10) outliers start: 15 outliers final: 14 residues processed: 86 average time/residue: 0.1331 time to fit residues: 15.0318 Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150147 restraints weight = 6473.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154443 restraints weight = 3038.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157167 restraints weight = 1763.476| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3933 Z= 0.204 Angle : 0.663 14.508 5353 Z= 0.331 Chirality : 0.039 0.122 619 Planarity : 0.004 0.037 660 Dihedral : 4.040 16.800 536 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.22 % Favored : 94.57 % Rotamer: Outliers : 4.47 % Allowed : 25.31 % Favored : 70.22 % 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: 1.37 (0.40), residues: 479 helix: 1.64 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.85 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 71 HIS 0.002 0.001 HIS A 137 PHE 0.023 0.002 PHE A 356 TYR 0.027 0.001 TYR A 284 ARG 0.002 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.96 seconds wall clock time: 24 minutes 54.37 seconds (1494.37 seconds total)