Starting phenix.real_space_refine on Tue Feb 13 06:41:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjl_36360/02_2024/8jjl_36360_neut_updated.pdb" } resolution = 3.2 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic. 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 20 5.16 5 C 1986 2.51 5 N 488 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3026 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'DZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.71 Number of scatterers: 3026 At special positions: 0 Unit cell: (55.76, 96.76, 92.66, 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 20 16.00 O 532 8.00 N 488 7.00 C 1986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " 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: 1.43 Conformation dependent library (CDL) restraints added in 590.5 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 30 through 60 Processing helix chain 'A' and resid 67 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 103 through 132 Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.665A pdb=" N SER A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 170 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 199 through 248 removed outlier: 4.571A pdb=" N VAL A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 3.502A pdb=" N THR A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 281 through 304 removed outlier: 3.505A pdb=" N PHE A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 365 removed outlier: 3.689A pdb=" N ALA A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 372 through 395 removed outlier: 4.591A pdb=" N SER A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 3.513A pdb=" N ARG A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 228 hydrogen bonds defined for protein. 684 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: 0.81 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 478 1.31 - 1.44: 851 1.44 - 1.56: 1735 1.56 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3095 Sorted by residual: bond pdb=" C TYR A 328 " pdb=" O TYR A 328 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" C ILE A 325 " pdb=" O ILE A 325 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N ALA A 323 " pdb=" CA ALA A 323 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.32e+00 bond pdb=" N PHE A 331 " pdb=" CA PHE A 331 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.76e+00 bond pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.28e-02 6.10e+03 5.76e+00 ... (remaining 3090 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.43: 41 105.43 - 112.58: 1623 112.58 - 119.72: 1045 119.72 - 126.87: 1457 126.87 - 134.02: 39 Bond angle restraints: 4205 Sorted by residual: angle pdb=" N ILE A 325 " pdb=" CA ILE A 325 " pdb=" C ILE A 325 " ideal model delta sigma weight residual 110.72 102.58 8.14 1.01e+00 9.80e-01 6.49e+01 angle pdb=" N LEU A 329 " pdb=" CA LEU A 329 " pdb=" C LEU A 329 " ideal model delta sigma weight residual 111.11 104.67 6.44 1.20e+00 6.94e-01 2.88e+01 angle pdb=" O ALA A 323 " pdb=" C ALA A 323 " pdb=" N TYR A 324 " ideal model delta sigma weight residual 122.33 129.34 -7.01 1.34e+00 5.57e-01 2.74e+01 angle pdb=" CA ALA A 323 " pdb=" C ALA A 323 " pdb=" N TYR A 324 " ideal model delta sigma weight residual 117.82 110.85 6.97 1.42e+00 4.96e-01 2.41e+01 angle pdb=" N LYS A 334 " pdb=" CA LYS A 334 " pdb=" C LYS A 334 " ideal model delta sigma weight residual 111.82 107.63 4.19 1.16e+00 7.43e-01 1.30e+01 ... (remaining 4200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.48: 1637 18.48 - 36.96: 157 36.96 - 55.44: 20 55.44 - 73.92: 4 73.92 - 92.40: 4 Dihedral angle restraints: 1822 sinusoidal: 714 harmonic: 1108 Sorted by residual: dihedral pdb=" CA HIS A 178 " pdb=" C HIS A 178 " pdb=" N GLN A 179 " pdb=" CA GLN A 179 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C TYR A 324 " pdb=" N TYR A 324 " pdb=" CA TYR A 324 " pdb=" CB TYR A 324 " ideal model delta harmonic sigma weight residual -122.60 -113.22 -9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CA ASP A 367 " pdb=" C ASP A 367 " pdb=" N ASN A 368 " pdb=" CA ASN A 368 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 401 0.055 - 0.110: 76 0.110 - 0.165: 7 0.165 - 0.220: 3 0.220 - 0.275: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" CA TYR A 324 " pdb=" N TYR A 324 " pdb=" C TYR A 324 " pdb=" CB TYR A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LEU A 233 " pdb=" N LEU A 233 " pdb=" C LEU A 233 " pdb=" CB LEU A 233 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A 325 " pdb=" CA ILE A 325 " pdb=" CG1 ILE A 325 " pdb=" CG2 ILE A 325 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 485 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 323 " -0.023 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C ALA A 323 " 0.089 2.00e-02 2.50e+03 pdb=" O ALA A 323 " -0.035 2.00e-02 2.50e+03 pdb=" N TYR A 324 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 227 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C LYS A 227 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS A 227 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 228 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 206 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL A 206 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 206 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 207 " 0.015 2.00e-02 2.50e+03 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 106 2.72 - 3.26: 3423 3.26 - 3.81: 5355 3.81 - 4.35: 6264 4.35 - 4.90: 10365 Nonbonded interactions: 25513 Sorted by model distance: nonbonded pdb=" OD2 ASP A 113 " pdb=" OH TYR A 383 " model vdw 2.173 2.440 nonbonded pdb=" OH TYR A 219 " pdb=" O LEU A 339 " model vdw 2.193 2.440 nonbonded pdb=" NZ LYS A 257 " pdb=" OD1 ASN A 303 " model vdw 2.279 2.520 nonbonded pdb=" O PHE A 139 " pdb=" OG SER A 143 " model vdw 2.323 2.440 nonbonded pdb=" OG1 THR A 118 " pdb=" OG SER A 207 " model vdw 2.338 2.440 ... (remaining 25508 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 5.520 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.004 0.050 3095 Z= 0.248 Angle : 0.752 8.138 4205 Z= 0.492 Chirality : 0.045 0.275 488 Planarity : 0.005 0.052 515 Dihedral : 14.770 92.404 1094 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.55 % Allowed : 0.93 % Favored : 97.52 % 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: 1.28 (0.46), residues: 371 helix: 1.35 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.68 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 380 HIS 0.005 0.001 HIS A 178 PHE 0.008 0.001 PHE A 357 TYR 0.031 0.002 TYR A 328 ARG 0.001 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 61 PHE cc_start: 0.7041 (m-10) cc_final: 0.6517 (m-10) REVERT: A 82 MET cc_start: 0.7587 (tmm) cc_final: 0.6999 (ttp) REVERT: A 151 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5952 (tpm170) outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 0.1454 time to fit residues: 17.7452 Evaluate side-chains 75 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 327 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 363 HIS ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3095 Z= 0.198 Angle : 0.568 6.564 4205 Z= 0.299 Chirality : 0.038 0.137 488 Planarity : 0.004 0.040 515 Dihedral : 8.874 73.013 416 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.48 % Allowed : 11.76 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.44), residues: 371 helix: 1.25 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.41 (0.90), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS A 172 PHE 0.009 0.001 PHE A 331 TYR 0.021 0.002 TYR A 328 ARG 0.002 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.365 Fit side-chains REVERT: A 61 PHE cc_start: 0.7148 (m-10) cc_final: 0.6022 (m-10) REVERT: A 82 MET cc_start: 0.7698 (tmm) cc_final: 0.7180 (ttm) REVERT: A 223 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6622 (m-80) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.1291 time to fit residues: 13.4730 Evaluate side-chains 80 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3095 Z= 0.209 Angle : 0.604 11.030 4205 Z= 0.307 Chirality : 0.039 0.258 488 Planarity : 0.003 0.033 515 Dihedral : 8.372 73.388 408 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.72 % Allowed : 12.38 % Favored : 83.90 % 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: 1.57 (0.44), residues: 371 helix: 1.36 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.39 (0.91), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 237 HIS 0.002 0.001 HIS A 172 PHE 0.007 0.001 PHE A 61 TYR 0.013 0.002 TYR A 328 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.353 Fit side-chains REVERT: A 82 MET cc_start: 0.7802 (tmm) cc_final: 0.7150 (ttp) REVERT: A 223 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6607 (m-80) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.1395 time to fit residues: 13.8450 Evaluate side-chains 77 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3095 Z= 0.218 Angle : 0.576 8.557 4205 Z= 0.297 Chirality : 0.039 0.193 488 Planarity : 0.003 0.028 515 Dihedral : 8.478 75.009 408 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.10 % Allowed : 12.69 % Favored : 84.21 % 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: 1.71 (0.45), residues: 371 helix: 1.48 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.52 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 237 HIS 0.003 0.001 HIS A 172 PHE 0.007 0.001 PHE A 208 TYR 0.027 0.002 TYR A 324 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.355 Fit side-chains REVERT: A 82 MET cc_start: 0.7880 (tmm) cc_final: 0.7345 (ttp) REVERT: A 223 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6652 (m-80) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.1255 time to fit residues: 12.6022 Evaluate side-chains 76 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3095 Z= 0.252 Angle : 0.588 7.321 4205 Z= 0.302 Chirality : 0.039 0.164 488 Planarity : 0.004 0.028 515 Dihedral : 8.689 78.415 408 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.33 % Allowed : 15.79 % Favored : 79.88 % 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: 1.70 (0.44), residues: 371 helix: 1.49 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.54 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 237 HIS 0.003 0.001 HIS A 172 PHE 0.007 0.001 PHE A 166 TYR 0.031 0.002 TYR A 324 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.308 Fit side-chains REVERT: A 82 MET cc_start: 0.7914 (tmm) cc_final: 0.7437 (ttp) REVERT: A 223 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6685 (m-80) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1175 time to fit residues: 11.6063 Evaluate side-chains 77 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3095 Z= 0.244 Angle : 0.592 8.001 4205 Z= 0.302 Chirality : 0.038 0.150 488 Planarity : 0.004 0.028 515 Dihedral : 8.561 76.380 408 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.95 % Allowed : 16.10 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.44), residues: 371 helix: 1.44 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.60 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 237 HIS 0.003 0.001 HIS A 172 PHE 0.008 0.001 PHE A 166 TYR 0.036 0.002 TYR A 324 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7858 (tmm) cc_final: 0.7397 (ttp) REVERT: A 223 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6706 (m-80) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.1144 time to fit residues: 11.6854 Evaluate side-chains 81 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3095 Z= 0.249 Angle : 0.591 6.884 4205 Z= 0.302 Chirality : 0.039 0.138 488 Planarity : 0.004 0.028 515 Dihedral : 8.589 77.004 408 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.33 % Allowed : 15.79 % Favored : 79.88 % 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: 1.51 (0.44), residues: 371 helix: 1.43 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.45 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 237 HIS 0.003 0.001 HIS A 172 PHE 0.008 0.001 PHE A 166 TYR 0.034 0.002 TYR A 324 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7856 (tmm) cc_final: 0.7459 (ttp) REVERT: A 223 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: A 300 LYS cc_start: 0.8337 (tptm) cc_final: 0.7853 (ttpp) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1524 time to fit residues: 15.0536 Evaluate side-chains 84 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3095 Z= 0.215 Angle : 0.606 6.071 4205 Z= 0.308 Chirality : 0.038 0.124 488 Planarity : 0.004 0.028 515 Dihedral : 8.459 75.010 408 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.26 % Allowed : 15.79 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.44), residues: 371 helix: 1.47 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.36 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 237 HIS 0.003 0.001 HIS A 172 PHE 0.007 0.001 PHE A 166 TYR 0.034 0.002 TYR A 324 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.7392 (ttt) cc_final: 0.7180 (ttm) REVERT: A 82 MET cc_start: 0.7849 (tmm) cc_final: 0.7392 (ttp) REVERT: A 223 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: A 300 LYS cc_start: 0.8311 (tptm) cc_final: 0.7821 (ttpp) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1232 time to fit residues: 12.7077 Evaluate side-chains 85 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3095 Z= 0.201 Angle : 0.598 5.596 4205 Z= 0.305 Chirality : 0.038 0.125 488 Planarity : 0.004 0.027 515 Dihedral : 8.305 73.149 408 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.64 % Allowed : 16.41 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.44), residues: 371 helix: 1.46 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.39 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 237 HIS 0.002 0.001 HIS A 172 PHE 0.007 0.001 PHE A 166 TYR 0.037 0.002 TYR A 324 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7885 (tmm) cc_final: 0.7383 (ttp) REVERT: A 223 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: A 300 LYS cc_start: 0.8273 (tptm) cc_final: 0.7813 (ttmt) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.1276 time to fit residues: 13.0013 Evaluate side-chains 86 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3095 Z= 0.199 Angle : 0.581 5.549 4205 Z= 0.301 Chirality : 0.038 0.126 488 Planarity : 0.004 0.026 515 Dihedral : 8.238 72.399 408 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.64 % Allowed : 16.10 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.44), residues: 371 helix: 1.51 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.48 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 237 HIS 0.002 0.001 HIS A 178 PHE 0.007 0.001 PHE A 166 TYR 0.038 0.002 TYR A 324 ARG 0.003 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7907 (tmm) cc_final: 0.7359 (ttp) REVERT: A 223 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: A 300 LYS cc_start: 0.8186 (tptm) cc_final: 0.7764 (ttpp) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.1317 time to fit residues: 13.4025 Evaluate side-chains 85 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 385 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 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 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114609 restraints weight = 4289.274| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.55 r_work: 0.3376 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3095 Z= 0.218 Angle : 0.588 5.589 4205 Z= 0.304 Chirality : 0.038 0.128 488 Planarity : 0.004 0.026 515 Dihedral : 8.307 73.278 408 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.72 % Allowed : 16.41 % Favored : 79.88 % 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: 1.63 (0.44), residues: 371 helix: 1.52 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.47 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 237 HIS 0.002 0.001 HIS A 178 PHE 0.007 0.001 PHE A 166 TYR 0.036 0.002 TYR A 324 ARG 0.003 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.92 seconds wall clock time: 22 minutes 15.13 seconds (1335.13 seconds total)