Starting phenix.real_space_refine on Fri Dec 27 07:05:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.map" model { file = "/net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c03_16354/12_2024/8c03_16354.cif" } resolution = 3.89 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= 0.028 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2187 2.51 5 N 542 2.21 5 O 574 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'SZU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.78 Number of scatterers: 3330 At special positions: 0 Unit cell: (78.12, 67.704, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 F 1 9.00 O 574 8.00 N 542 7.00 C 2187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 436.3 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.634A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.723A pdb=" N LEU A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.826A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.742A pdb=" N GLY A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 451 through 483 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.815A pdb=" N ASN A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.118A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 921 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: 0.94 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1028 1.34 - 1.46: 824 1.46 - 1.58: 1505 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 3401 Sorted by residual: bond pdb=" C1 SZU A 601 " pdb=" C8 SZU A 601 " ideal model delta sigma weight residual 1.476 1.325 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.517 1.377 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.413 1.335 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C8 SZU A 601 " pdb=" N6 SZU A 601 " ideal model delta sigma weight residual 1.396 1.329 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C20 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.395 1.328 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 4565 2.51 - 5.03: 58 5.03 - 7.54: 2 7.54 - 10.06: 1 10.06 - 12.57: 1 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C3 SZU A 601 " pdb=" C2 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 113.72 101.15 12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N GLN A 496 " pdb=" CA GLN A 496 " pdb=" C GLN A 496 " ideal model delta sigma weight residual 111.36 106.91 4.45 1.09e+00 8.42e-01 1.67e+01 angle pdb=" N LEU A 59 " pdb=" CA LEU A 59 " pdb=" C LEU A 59 " ideal model delta sigma weight residual 111.11 106.50 4.61 1.20e+00 6.94e-01 1.48e+01 angle pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" O THR A 334 " ideal model delta sigma weight residual 120.90 117.00 3.90 1.03e+00 9.43e-01 1.43e+01 angle pdb=" N PHE A 324 " pdb=" CA PHE A 324 " pdb=" C PHE A 324 " ideal model delta sigma weight residual 111.71 106.79 4.92 1.34e+00 5.57e-01 1.35e+01 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1769 14.30 - 28.61: 130 28.61 - 42.91: 44 42.91 - 57.21: 17 57.21 - 71.52: 6 Dihedral angle restraints: 1966 sinusoidal: 737 harmonic: 1229 Sorted by residual: dihedral pdb=" N GLU A 518 " pdb=" CA GLU A 518 " pdb=" CB GLU A 518 " pdb=" CG GLU A 518 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sinusoidal sigma weight residual 180.00 123.89 56.11 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" CB ILE A 78 " pdb=" CG1 ILE A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -114.35 54.35 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 473 0.052 - 0.104: 74 0.104 - 0.156: 9 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA LEU A 59 " pdb=" N LEU A 59 " pdb=" C LEU A 59 " pdb=" CB LEU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 333 " pdb=" N TYR A 333 " pdb=" C TYR A 333 " pdb=" CB TYR A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 324 " pdb=" N PHE A 324 " pdb=" C PHE A 324 " pdb=" CB PHE A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 557 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A 53 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 53 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 54 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 324 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C PHE A 324 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 324 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 325 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 SZU A 601 " -0.004 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C2 SZU A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C8 SZU A 601 " 0.013 2.00e-02 2.50e+03 pdb=" N1 SZU A 601 " -0.023 2.00e-02 2.50e+03 pdb=" O1 SZU A 601 " -0.002 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 1 1.97 - 2.70: 81 2.70 - 3.43: 5414 3.43 - 4.17: 7309 4.17 - 4.90: 13846 Nonbonded interactions: 26651 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 3.040 nonbonded pdb=" CD1 LEU A 469 " pdb=" F1 SZU A 601 " model vdw 2.141 3.410 nonbonded pdb=" O TYR A 20 " pdb=" OG SER A 23 " model vdw 2.205 3.040 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 3.120 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 3.040 ... (remaining 26646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 3401 Z= 0.430 Angle : 0.670 12.575 4627 Z= 0.403 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 13.116 71.516 1178 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.06 % Allowed : 8.08 % Favored : 88.86 % 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: 2.75 (0.41), residues: 423 helix: 2.29 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -0.88 (0.85), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.003 0.001 HIS A 32 PHE 0.008 0.001 PHE A 508 TYR 0.006 0.001 TYR A 220 ARG 0.001 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7974 (tptt) cc_final: 0.7485 (tppt) REVERT: A 100 ASN cc_start: 0.7632 (m-40) cc_final: 0.6460 (m-40) REVERT: A 216 MET cc_start: 0.8280 (tpt) cc_final: 0.7925 (tpp) REVERT: A 319 MET cc_start: 0.7296 (ttt) cc_final: 0.6959 (tmm) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1377 time to fit residues: 23.3363 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 174 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 HIS A 194 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.227 Angle : 0.580 6.753 4627 Z= 0.300 Chirality : 0.039 0.135 560 Planarity : 0.004 0.028 556 Dihedral : 7.431 75.543 476 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 18.11 % Favored : 78.27 % 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: 3.07 (0.40), residues: 423 helix: 2.31 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.08 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.003 0.001 HIS A 32 PHE 0.026 0.002 PHE A 308 TYR 0.013 0.002 TYR A 29 ARG 0.008 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.383 Fit side-chains REVERT: A 90 LYS cc_start: 0.8030 (tptt) cc_final: 0.7473 (tppt) REVERT: A 166 ASP cc_start: 0.8193 (t0) cc_final: 0.7808 (t0) REVERT: A 173 MET cc_start: 0.7616 (ttm) cc_final: 0.7263 (ttm) REVERT: A 319 MET cc_start: 0.7473 (ttt) cc_final: 0.7099 (tmm) REVERT: A 366 LYS cc_start: 0.8316 (tptt) cc_final: 0.7867 (mmmt) REVERT: A 469 LEU cc_start: 0.8884 (tp) cc_final: 0.8623 (tp) outliers start: 13 outliers final: 4 residues processed: 113 average time/residue: 0.1406 time to fit residues: 19.6486 Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.213 Angle : 0.583 6.754 4627 Z= 0.301 Chirality : 0.039 0.158 560 Planarity : 0.003 0.028 556 Dihedral : 6.932 73.884 470 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.79 % Allowed : 20.89 % Favored : 76.32 % 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: 2.93 (0.40), residues: 423 helix: 2.24 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.26 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 43 PHE 0.023 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.369 Fit side-chains REVERT: A 57 SER cc_start: 0.8258 (m) cc_final: 0.7865 (p) REVERT: A 166 ASP cc_start: 0.8115 (t0) cc_final: 0.7675 (t0) REVERT: A 319 MET cc_start: 0.7632 (ttt) cc_final: 0.7200 (tmm) REVERT: A 366 LYS cc_start: 0.8375 (tptt) cc_final: 0.7958 (mmmt) REVERT: A 457 LEU cc_start: 0.7701 (tp) cc_final: 0.7493 (tp) REVERT: A 543 GLN cc_start: 0.7825 (mm110) cc_final: 0.7526 (mm-40) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1308 time to fit residues: 17.9573 Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3401 Z= 0.236 Angle : 0.595 6.504 4627 Z= 0.306 Chirality : 0.039 0.149 560 Planarity : 0.003 0.032 556 Dihedral : 6.854 73.354 470 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.01 % Allowed : 20.61 % Favored : 74.37 % 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: 2.85 (0.40), residues: 423 helix: 2.20 (0.25), residues: 370 sheet: None (None), residues: 0 loop : -0.36 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.007 0.002 HIS A 535 PHE 0.036 0.002 PHE A 308 TYR 0.025 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.379 Fit side-chains REVERT: A 57 SER cc_start: 0.7988 (m) cc_final: 0.7716 (p) REVERT: A 166 ASP cc_start: 0.8143 (t0) cc_final: 0.7673 (t0) REVERT: A 319 MET cc_start: 0.7634 (ttt) cc_final: 0.7134 (tmm) REVERT: A 366 LYS cc_start: 0.8376 (tptt) cc_final: 0.7986 (mmmt) REVERT: A 543 GLN cc_start: 0.7885 (mm110) cc_final: 0.7561 (mm-40) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.1365 time to fit residues: 19.6462 Evaluate side-chains 115 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3401 Z= 0.257 Angle : 0.637 7.376 4627 Z= 0.320 Chirality : 0.039 0.185 560 Planarity : 0.003 0.032 556 Dihedral : 6.771 71.971 470 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.13 % Allowed : 22.56 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.40), residues: 423 helix: 2.11 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.31 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 535 PHE 0.029 0.002 PHE A 308 TYR 0.024 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.410 Fit side-chains REVERT: A 100 ASN cc_start: 0.8644 (m-40) cc_final: 0.8174 (m-40) REVERT: A 166 ASP cc_start: 0.8098 (t0) cc_final: 0.7645 (t0) REVERT: A 319 MET cc_start: 0.7665 (ttt) cc_final: 0.7184 (tmm) REVERT: A 499 MET cc_start: 0.8620 (ttp) cc_final: 0.8294 (ttt) REVERT: A 504 ASP cc_start: 0.8088 (t70) cc_final: 0.7719 (t0) REVERT: A 543 GLN cc_start: 0.7867 (mm110) cc_final: 0.7532 (mm-40) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.1315 time to fit residues: 18.2864 Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 212 ASN A 380 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3401 Z= 0.254 Angle : 0.651 8.289 4627 Z= 0.328 Chirality : 0.040 0.179 560 Planarity : 0.003 0.034 556 Dihedral : 6.679 70.549 470 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.29 % Allowed : 23.96 % Favored : 70.75 % 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: 2.83 (0.40), residues: 423 helix: 2.15 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.21 (1.01), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 535 PHE 0.030 0.002 PHE A 308 TYR 0.022 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.353 Fit side-chains REVERT: A 100 ASN cc_start: 0.8566 (m-40) cc_final: 0.7806 (m-40) REVERT: A 145 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 166 ASP cc_start: 0.8126 (t0) cc_final: 0.7677 (t0) REVERT: A 319 MET cc_start: 0.7745 (ttt) cc_final: 0.7257 (tmm) REVERT: A 366 LYS cc_start: 0.8429 (tptt) cc_final: 0.8085 (tmtt) REVERT: A 504 ASP cc_start: 0.8099 (t70) cc_final: 0.7719 (t0) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.1329 time to fit residues: 17.7267 Evaluate side-chains 108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3401 Z= 0.237 Angle : 0.648 8.846 4627 Z= 0.324 Chirality : 0.040 0.176 560 Planarity : 0.003 0.032 556 Dihedral : 6.602 69.463 470 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.29 % Allowed : 24.23 % Favored : 70.47 % 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: 2.81 (0.40), residues: 423 helix: 2.14 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.25 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.005 0.001 HIS A 43 PHE 0.028 0.002 PHE A 308 TYR 0.021 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.343 Fit side-chains REVERT: A 166 ASP cc_start: 0.8094 (t0) cc_final: 0.7887 (t0) REVERT: A 319 MET cc_start: 0.7726 (ttt) cc_final: 0.7255 (tmm) REVERT: A 366 LYS cc_start: 0.8459 (tptt) cc_final: 0.8048 (tmtt) REVERT: A 392 PHE cc_start: 0.7909 (t80) cc_final: 0.7665 (t80) REVERT: A 504 ASP cc_start: 0.8082 (t70) cc_final: 0.7698 (t0) REVERT: A 543 GLN cc_start: 0.7879 (mm110) cc_final: 0.7573 (mm-40) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.1270 time to fit residues: 16.8831 Evaluate side-chains 107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 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 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.234 Angle : 0.645 9.153 4627 Z= 0.323 Chirality : 0.040 0.180 560 Planarity : 0.003 0.033 556 Dihedral : 6.544 68.633 470 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.18 % Allowed : 25.35 % Favored : 70.47 % 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: 2.83 (0.40), residues: 423 helix: 2.15 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.23 (1.01), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS A 32 PHE 0.031 0.002 PHE A 308 TYR 0.024 0.002 TYR A 29 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.423 Fit side-chains REVERT: A 166 ASP cc_start: 0.8033 (t0) cc_final: 0.7829 (t0) REVERT: A 202 VAL cc_start: 0.8470 (m) cc_final: 0.8266 (p) REVERT: A 319 MET cc_start: 0.7708 (ttt) cc_final: 0.7258 (tmm) REVERT: A 366 LYS cc_start: 0.8367 (tptt) cc_final: 0.7917 (mmmt) REVERT: A 392 PHE cc_start: 0.7879 (t80) cc_final: 0.7624 (t80) REVERT: A 504 ASP cc_start: 0.8068 (t70) cc_final: 0.7688 (t0) outliers start: 15 outliers final: 14 residues processed: 100 average time/residue: 0.1381 time to fit residues: 17.4471 Evaluate side-chains 103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3401 Z= 0.204 Angle : 0.625 9.885 4627 Z= 0.311 Chirality : 0.039 0.180 560 Planarity : 0.004 0.032 556 Dihedral : 6.397 67.997 470 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.06 % Allowed : 26.18 % Favored : 70.75 % 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: 2.92 (0.40), residues: 423 helix: 2.25 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.62 (0.95), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.003 0.001 HIS A 32 PHE 0.032 0.002 PHE A 308 TYR 0.010 0.001 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.389 Fit side-chains REVERT: A 166 ASP cc_start: 0.8062 (t0) cc_final: 0.7599 (t0) REVERT: A 202 VAL cc_start: 0.8376 (m) cc_final: 0.8163 (p) REVERT: A 319 MET cc_start: 0.7546 (ttt) cc_final: 0.7170 (tmm) REVERT: A 366 LYS cc_start: 0.8458 (tptt) cc_final: 0.7944 (mmmt) REVERT: A 392 PHE cc_start: 0.7862 (t80) cc_final: 0.7627 (t80) REVERT: A 504 ASP cc_start: 0.7949 (t70) cc_final: 0.7617 (t0) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.1248 time to fit residues: 15.7161 Evaluate side-chains 101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.219 Angle : 0.646 10.118 4627 Z= 0.324 Chirality : 0.041 0.193 560 Planarity : 0.004 0.032 556 Dihedral : 6.365 66.387 470 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.34 % Allowed : 27.30 % Favored : 69.36 % 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: 2.85 (0.40), residues: 423 helix: 2.17 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.33 (0.97), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 42 HIS 0.006 0.001 HIS A 43 PHE 0.037 0.002 PHE A 308 TYR 0.009 0.001 TYR A 54 ARG 0.002 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.379 Fit side-chains REVERT: A 166 ASP cc_start: 0.8000 (t0) cc_final: 0.7558 (t0) REVERT: A 319 MET cc_start: 0.7467 (ttt) cc_final: 0.7002 (tmm) REVERT: A 392 PHE cc_start: 0.7813 (t80) cc_final: 0.7584 (t80) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.1328 time to fit residues: 16.7125 Evaluate side-chains 103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.178491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143769 restraints weight = 4784.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148348 restraints weight = 3074.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151408 restraints weight = 2336.159| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3401 Z= 0.252 Angle : 0.682 10.586 4627 Z= 0.340 Chirality : 0.041 0.193 560 Planarity : 0.004 0.032 556 Dihedral : 6.408 64.743 470 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.18 % Allowed : 27.86 % Favored : 67.97 % 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: 2.69 (0.40), residues: 423 helix: 2.05 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.25 (0.98), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 42 HIS 0.003 0.001 HIS A 32 PHE 0.026 0.002 PHE A 292 TYR 0.010 0.001 TYR A 54 ARG 0.003 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.13 seconds wall clock time: 20 minutes 48.10 seconds (1248.10 seconds total)