Starting phenix.real_space_refine on Sun Mar 10 16:44:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/03_2024/8c03_16354_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3330 Unusual residues: {'SZU': 1} Classifications: {'peptide': 429, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 419, None: 1} Not linked: pdbres="LYS A 549 " pdbres="SZU A 601 " Chain breaks: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.68 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 - 3.50 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: 1.30 Conformation dependent library (CDL) restraints added in 797.8 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 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 88 through 115 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 126 through 155 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 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) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 486 through 513 removed outlier: 3.690A pdb=" N ARG A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 493 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 545 279 hydrogen bonds defined for protein. 777 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: 0.88 Time building geometry restraints manager: 1.41 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 1.547 1.325 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.558 1.377 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C1 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 1.455 1.329 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C16 SZU A 601 " pdb=" C17 SZU A 601 " ideal model delta sigma weight residual 1.417 1.329 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C9 SZU A 601 " pdb=" O2 SZU A 601 " ideal model delta sigma weight residual 1.333 1.405 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.55: 75 106.55 - 113.40: 1952 113.40 - 120.25: 1289 120.25 - 127.10: 1271 127.10 - 133.95: 40 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N4 SZU A 601 " ideal model delta sigma weight residual 144.40 125.60 18.80 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N5 SZU A 601 " ideal model delta sigma weight residual 105.58 124.12 -18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" C11 SZU A 601 " pdb=" C10 SZU A 601 " pdb=" N6 SZU A 601 " ideal model delta sigma weight residual 139.27 123.98 15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" C11 SZU A 601 " pdb=" C10 SZU A 601 " pdb=" O2 SZU A 601 " ideal model delta sigma weight residual 110.79 125.74 -14.95 3.00e+00 1.11e-01 2.48e+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 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1807 16.29 - 32.58: 109 32.58 - 48.87: 31 48.87 - 65.16: 11 65.16 - 81.45: 2 Dihedral angle restraints: 1960 sinusoidal: 731 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 1957 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: 83 2.70 - 3.43: 5442 3.43 - 4.17: 7372 4.17 - 4.90: 13869 Nonbonded interactions: 26767 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 2.440 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 2.440 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 2.520 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 2.440 ... (remaining 26762 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: 0.240 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: 1.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- 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 : 0.007 0.222 3401 Z= 0.448 Angle : 0.858 18.796 4627 Z= 0.441 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 12.868 81.455 1172 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 fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.363 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: 0.1345 time to fit residues: 22.7595 Evaluate side-chains 104 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 43 random chunks: chunk 36 optimal weight: 0.0030 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3401 Z= 0.197 Angle : 0.563 8.758 4627 Z= 0.287 Chirality : 0.037 0.125 560 Planarity : 0.004 0.025 556 Dihedral : 6.033 51.276 470 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.18 % Allowed : 16.71 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.40), residues: 423 helix: 2.26 (0.26), residues: 366 sheet: None (None), residues: 0 loop : -0.25 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 299 HIS 0.003 0.001 HIS A 32 PHE 0.029 0.002 PHE A 308 TYR 0.014 0.001 TYR A 29 ARG 0.009 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 118 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7907 (tptt) cc_final: 0.7398 (tppt) REVERT: A 173 MET cc_start: 0.7609 (ttm) cc_final: 0.7252 (ttm) REVERT: A 457 LEU cc_start: 0.7800 (tp) cc_final: 0.7582 (tp) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.1256 time to fit residues: 17.5374 Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 112 MET Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3401 Z= 0.317 Angle : 0.627 8.910 4627 Z= 0.318 Chirality : 0.039 0.157 560 Planarity : 0.004 0.021 556 Dihedral : 6.088 57.115 466 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.01 % Allowed : 19.22 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.41), residues: 423 helix: 2.00 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -0.10 (1.02), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.005 0.001 HIS A 32 PHE 0.021 0.002 PHE A 308 TYR 0.017 0.002 TYR A 29 ARG 0.001 0.000 ARG A 489 *********************** 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 121 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.329 Fit side-chains REVERT: A 173 MET cc_start: 0.7599 (ttm) cc_final: 0.7393 (ttm) REVERT: A 319 MET cc_start: 0.7568 (tmm) cc_final: 0.6891 (tmm) REVERT: A 322 LEU cc_start: 0.8823 (mm) cc_final: 0.8603 (mp) REVERT: A 457 LEU cc_start: 0.8019 (tp) cc_final: 0.7775 (tp) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.1107 time to fit residues: 16.1105 Evaluate side-chains 116 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 134 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 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 389 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 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 212 ASN ** 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: 0.7610 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3401 Z= 0.223 Angle : 0.573 7.208 4627 Z= 0.292 Chirality : 0.037 0.164 560 Planarity : 0.004 0.022 556 Dihedral : 5.900 60.460 466 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.46 % Allowed : 21.73 % Favored : 73.82 % 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: 2.50 (0.41), residues: 423 helix: 2.03 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -0.67 (0.93), residues: 59 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 0.012 0.001 PHE A 308 TYR 0.018 0.002 TYR A 29 ARG 0.002 0.000 ARG A 293 *********************** 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 fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.372 Fit side-chains REVERT: A 173 MET cc_start: 0.7620 (ttm) cc_final: 0.7218 (ttm) REVERT: A 322 LEU cc_start: 0.8808 (mm) cc_final: 0.8554 (mp) REVERT: A 457 LEU cc_start: 0.8058 (tp) cc_final: 0.7819 (tp) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.1180 time to fit residues: 16.8397 Evaluate side-chains 113 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7591 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3401 Z= 0.202 Angle : 0.560 6.139 4627 Z= 0.287 Chirality : 0.037 0.148 560 Planarity : 0.003 0.023 556 Dihedral : 5.511 61.611 464 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.46 % Allowed : 22.28 % Favored : 73.26 % 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: 2.49 (0.41), residues: 423 helix: 2.02 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.72 (0.92), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 299 HIS 0.003 0.001 HIS A 32 PHE 0.015 0.001 PHE A 392 TYR 0.026 0.002 TYR A 29 ARG 0.002 0.000 ARG A 179 *********************** 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 120 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.356 Fit side-chains REVERT: A 100 ASN cc_start: 0.8631 (m-40) cc_final: 0.8203 (m-40) REVERT: A 173 MET cc_start: 0.7450 (ttm) cc_final: 0.7228 (ttm) REVERT: A 319 MET cc_start: 0.7650 (tmm) cc_final: 0.6917 (tmm) REVERT: A 322 LEU cc_start: 0.8890 (mm) cc_final: 0.8612 (mp) REVERT: A 457 LEU cc_start: 0.8050 (tp) cc_final: 0.7795 (tp) REVERT: A 491 ILE cc_start: 0.8773 (tp) cc_final: 0.8529 (tt) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.1213 time to fit residues: 17.6093 Evaluate side-chains 109 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7610 moved from start: 0.3500 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= 0.231 Angle : 0.597 7.976 4627 Z= 0.304 Chirality : 0.038 0.185 560 Planarity : 0.003 0.021 556 Dihedral : 5.475 61.431 464 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.18 % Allowed : 22.84 % Favored : 72.98 % 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: 2.36 (0.41), residues: 423 helix: 1.94 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.79 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 299 HIS 0.005 0.001 HIS A 535 PHE 0.016 0.001 PHE A 539 TYR 0.022 0.002 TYR A 29 ARG 0.001 0.000 ARG A 179 *********************** 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 113 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.436 Fit side-chains REVERT: A 319 MET cc_start: 0.7700 (tmm) cc_final: 0.7016 (tmm) REVERT: A 322 LEU cc_start: 0.8926 (mm) cc_final: 0.8665 (mp) REVERT: A 457 LEU cc_start: 0.7980 (tp) cc_final: 0.7731 (tp) REVERT: A 491 ILE cc_start: 0.8834 (tp) cc_final: 0.8603 (tt) outliers start: 15 outliers final: 14 residues processed: 109 average time/residue: 0.1285 time to fit residues: 17.8316 Evaluate side-chains 108 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7597 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.219 Angle : 0.588 7.572 4627 Z= 0.299 Chirality : 0.038 0.180 560 Planarity : 0.003 0.021 556 Dihedral : 5.407 61.058 464 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.90 % Allowed : 24.23 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.41), residues: 423 helix: 1.97 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -0.75 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 299 HIS 0.005 0.001 HIS A 535 PHE 0.022 0.002 PHE A 392 TYR 0.021 0.002 TYR A 29 ARG 0.001 0.000 ARG A 179 *********************** 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 110 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.336 Fit side-chains REVERT: A 84 ASP cc_start: 0.7837 (p0) cc_final: 0.7625 (p0) REVERT: A 322 LEU cc_start: 0.8964 (mm) cc_final: 0.8690 (mp) REVERT: A 457 LEU cc_start: 0.7967 (tp) cc_final: 0.7709 (tp) REVERT: A 491 ILE cc_start: 0.8840 (tp) cc_final: 0.8566 (tt) outliers start: 14 outliers final: 13 residues processed: 105 average time/residue: 0.1229 time to fit residues: 16.3553 Evaluate side-chains 106 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** 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: 0.7575 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3401 Z= 0.202 Angle : 0.579 7.132 4627 Z= 0.293 Chirality : 0.038 0.179 560 Planarity : 0.003 0.022 556 Dihedral : 5.366 60.805 464 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.74 % Allowed : 23.96 % 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: 2.38 (0.42), residues: 423 helix: 1.96 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -0.77 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 299 HIS 0.004 0.001 HIS A 535 PHE 0.014 0.001 PHE A 539 TYR 0.021 0.001 TYR A 29 ARG 0.001 0.000 ARG A 179 *********************** 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 112 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.362 Fit side-chains REVERT: A 84 ASP cc_start: 0.7851 (p0) cc_final: 0.7607 (p0) REVERT: A 112 MET cc_start: 0.7958 (mmm) cc_final: 0.7616 (mmp) REVERT: A 319 MET cc_start: 0.7681 (tmm) cc_final: 0.6754 (tmm) REVERT: A 322 LEU cc_start: 0.8988 (mm) cc_final: 0.8753 (mp) REVERT: A 457 LEU cc_start: 0.7917 (tp) cc_final: 0.7664 (tp) REVERT: A 491 ILE cc_start: 0.8838 (tp) cc_final: 0.8556 (tt) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.1276 time to fit residues: 17.3060 Evaluate side-chains 106 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.218 Angle : 0.590 7.578 4627 Z= 0.299 Chirality : 0.037 0.182 560 Planarity : 0.004 0.058 556 Dihedral : 5.361 60.412 464 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.18 % Allowed : 24.51 % 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: 2.43 (0.42), residues: 423 helix: 1.99 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.71 (0.93), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.004 0.001 HIS A 43 PHE 0.028 0.002 PHE A 539 TYR 0.020 0.001 TYR A 29 ARG 0.001 0.000 ARG A 179 *********************** 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 109 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.323 Fit side-chains REVERT: A 84 ASP cc_start: 0.7822 (p0) cc_final: 0.7553 (p0) REVERT: A 319 MET cc_start: 0.7678 (tmm) cc_final: 0.6796 (tmm) REVERT: A 457 LEU cc_start: 0.7966 (tp) cc_final: 0.7717 (tp) REVERT: A 491 ILE cc_start: 0.8845 (tp) cc_final: 0.8561 (tt) outliers start: 15 outliers final: 13 residues processed: 105 average time/residue: 0.1186 time to fit residues: 15.7184 Evaluate side-chains 103 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 174 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 0.0770 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.193 Angle : 0.590 8.116 4627 Z= 0.299 Chirality : 0.038 0.180 560 Planarity : 0.004 0.054 556 Dihedral : 5.320 59.692 464 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.23 % Allowed : 27.58 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.42), residues: 423 helix: 2.08 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.92 (0.91), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.003 0.001 HIS A 43 PHE 0.015 0.001 PHE A 539 TYR 0.012 0.001 TYR A 29 ARG 0.004 0.000 ARG A 179 ********************** 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 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.380 Fit side-chains REVERT: A 84 ASP cc_start: 0.7791 (p0) cc_final: 0.7494 (p0) REVERT: A 319 MET cc_start: 0.7866 (tmm) cc_final: 0.7106 (tmm) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.1289 time to fit residues: 15.6408 Evaluate side-chains 95 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 58 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 Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144534 restraints weight = 4750.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149051 restraints weight = 3064.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151631 restraints weight = 2345.571| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4056 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= 0.228 Angle : 0.637 11.388 4627 Z= 0.317 Chirality : 0.038 0.178 560 Planarity : 0.004 0.048 556 Dihedral : 5.283 59.636 464 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 28.13 % Favored : 68.80 % 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: 2.48 (0.42), residues: 423 helix: 2.05 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.80 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 42 HIS 0.004 0.001 HIS A 43 PHE 0.028 0.002 PHE A 539 TYR 0.011 0.001 TYR A 29 ARG 0.002 0.000 ARG A 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1047.40 seconds wall clock time: 19 minutes 43.07 seconds (1183.07 seconds total)