Starting phenix.real_space_refine on Thu Jul 18 18:23:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/07_2024/8wlm_37624.cif" } resolution = 3.57 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= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1860 2.51 5 N 436 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2804 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2791 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.53, per 1000 atoms: 0.90 Number of scatterers: 2804 At special positions: 0 Unit cell: (68.968, 66.172, 68.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 480 8.00 N 436 7.00 C 1860 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: 2.19 Conformation dependent library (CDL) restraints added in 704.8 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 688 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 88.5% 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 18 through 50 removed outlier: 3.606A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 132 through 156 Proline residue: A 147 - end of helix removed outlier: 3.882A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.655A pdb=" N ILE A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.895A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.822A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.602A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.590A pdb=" N LEU A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 removed outlier: 3.695A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.027A pdb=" N MET A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 356 removed outlier: 4.574A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 3.881A pdb=" N ILE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 381 through 414 removed outlier: 4.277A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.102A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.625A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 663 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: 0.75 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 827 1.34 - 1.46: 386 1.46 - 1.57: 1606 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2867 Sorted by residual: bond pdb=" CA SRO A 501 " pdb=" NZ SRO A 501 " ideal model delta sigma weight residual 1.469 1.415 0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" CD2 SRO A 501 " pdb=" CE2 SRO A 501 " ideal model delta sigma weight residual 1.419 1.368 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" CA SRO A 501 " pdb=" CB SRO A 501 " ideal model delta sigma weight residual 1.524 1.569 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" CZ3 SRO A 501 " pdb=" CH2 SRO A 501 " ideal model delta sigma weight residual 1.407 1.375 0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.06e-02 8.90e+03 2.17e+00 ... (remaining 2862 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.32: 113 106.32 - 113.28: 1564 113.28 - 120.24: 1102 120.24 - 127.19: 1096 127.19 - 134.15: 32 Bond angle restraints: 3907 Sorted by residual: angle pdb=" CB MET A 402 " pdb=" CG MET A 402 " pdb=" SD MET A 402 " ideal model delta sigma weight residual 112.70 103.66 9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" C ILE A 265 " pdb=" N GLN A 266 " pdb=" CA GLN A 266 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.64e+00 angle pdb=" CA PRO A 236 " pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 117.93 121.20 -3.27 1.20e+00 6.94e-01 7.43e+00 angle pdb=" CA MET A 402 " pdb=" CB MET A 402 " pdb=" CG MET A 402 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.72e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.80 -3.10 1.22e+00 6.72e-01 6.45e+00 ... (remaining 3902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 1519 17.32 - 34.65: 119 34.65 - 51.97: 36 51.97 - 69.29: 4 69.29 - 86.61: 4 Dihedral angle restraints: 1682 sinusoidal: 604 harmonic: 1078 Sorted by residual: dihedral pdb=" CA MET A 402 " pdb=" C MET A 402 " pdb=" N MET A 403 " pdb=" CA MET A 403 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 86.61 -86.61 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " pdb=" OE1 GLU A 312 " ideal model delta sinusoidal sigma weight residual 0.00 -77.86 77.86 1 3.00e+01 1.11e-03 8.42e+00 ... (remaining 1679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 278 0.031 - 0.062: 116 0.062 - 0.093: 49 0.093 - 0.123: 25 0.123 - 0.154: 9 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA THR A 322 " pdb=" N THR A 322 " pdb=" C THR A 322 " pdb=" CB THR A 322 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA CYS A 430 " pdb=" N CYS A 430 " pdb=" C CYS A 430 " pdb=" CB CYS A 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 474 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 348 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C PHE A 348 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 348 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 349 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 449 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 450 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 265 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ILE A 265 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE A 265 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN A 266 " 0.008 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 240 2.74 - 3.28: 3112 3.28 - 3.82: 4822 3.82 - 4.36: 5261 4.36 - 4.90: 9305 Nonbonded interactions: 22740 Sorted by model distance: nonbonded pdb=" O MET A 175 " pdb=" OG SER A 179 " model vdw 2.198 2.440 nonbonded pdb=" OE2 GLU A 215 " pdb=" ND1 HIS A 353 " model vdw 2.424 2.520 nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.426 2.520 nonbonded pdb=" OD2 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.464 2.520 nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.501 2.440 ... (remaining 22735 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: 0.450 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2867 Z= 0.279 Angle : 0.798 9.042 3907 Z= 0.391 Chirality : 0.046 0.154 477 Planarity : 0.005 0.036 481 Dihedral : 14.404 86.614 994 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.43), residues: 378 helix: 0.86 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -1.79 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.022 0.002 PHE A 463 TYR 0.015 0.002 TYR A 422 ARG 0.004 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.271 Fit side-chains REVERT: A 166 PHE cc_start: 0.7621 (m-80) cc_final: 0.7236 (m-80) REVERT: A 194 ILE cc_start: 0.8531 (mm) cc_final: 0.8160 (mm) REVERT: A 198 CYS cc_start: 0.8432 (p) cc_final: 0.8164 (p) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1018 time to fit residues: 13.4534 Evaluate side-chains 93 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2867 Z= 0.209 Angle : 0.681 7.922 3907 Z= 0.334 Chirality : 0.042 0.137 477 Planarity : 0.005 0.033 481 Dihedral : 6.387 66.183 401 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 16.67 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.44), residues: 378 helix: 1.08 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.05 (0.69), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.018 0.002 PHE A 348 TYR 0.018 0.001 TYR A 422 ARG 0.005 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.275 Fit side-chains REVERT: A 166 PHE cc_start: 0.7585 (m-80) cc_final: 0.7233 (m-80) REVERT: A 198 CYS cc_start: 0.8329 (p) cc_final: 0.8115 (p) REVERT: A 204 MET cc_start: 0.8719 (mmt) cc_final: 0.8445 (mmt) REVERT: A 230 MET cc_start: 0.7494 (ttm) cc_final: 0.7165 (ttm) REVERT: A 286 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 353 HIS cc_start: 0.8643 (t-170) cc_final: 0.7952 (t-170) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.0981 time to fit residues: 12.8525 Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2867 Z= 0.217 Angle : 0.674 8.195 3907 Z= 0.329 Chirality : 0.042 0.140 477 Planarity : 0.004 0.036 481 Dihedral : 5.986 59.512 401 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.06 % Allowed : 21.77 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.44), residues: 378 helix: 1.15 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.88 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.302 Fit side-chains REVERT: A 166 PHE cc_start: 0.7522 (m-80) cc_final: 0.7170 (m-80) REVERT: A 204 MET cc_start: 0.8730 (mmt) cc_final: 0.8400 (mmt) REVERT: A 230 MET cc_start: 0.7432 (ttm) cc_final: 0.7102 (ttm) REVERT: A 286 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 353 HIS cc_start: 0.8636 (t-170) cc_final: 0.7996 (t-170) REVERT: A 355 MET cc_start: 0.8245 (tmm) cc_final: 0.7735 (tmm) REVERT: A 365 MET cc_start: 0.7884 (mtp) cc_final: 0.7633 (mmm) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.0927 time to fit residues: 12.1074 Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2867 Z= 0.211 Angle : 0.671 8.190 3907 Z= 0.325 Chirality : 0.042 0.142 477 Planarity : 0.004 0.035 481 Dihedral : 5.844 56.474 401 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.74 % Allowed : 25.85 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.44), residues: 378 helix: 1.19 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.273 Fit side-chains REVERT: A 166 PHE cc_start: 0.7598 (m-80) cc_final: 0.7158 (m-80) REVERT: A 204 MET cc_start: 0.8720 (mmt) cc_final: 0.8371 (mmt) REVERT: A 230 MET cc_start: 0.7439 (ttm) cc_final: 0.7097 (ttm) REVERT: A 286 THR cc_start: 0.8579 (m) cc_final: 0.8214 (p) REVERT: A 353 HIS cc_start: 0.8642 (t-170) cc_final: 0.8077 (t-170) REVERT: A 355 MET cc_start: 0.8302 (tmm) cc_final: 0.7800 (tmm) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 0.0900 time to fit residues: 11.7433 Evaluate side-chains 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2867 Z= 0.211 Angle : 0.684 8.727 3907 Z= 0.328 Chirality : 0.043 0.142 477 Planarity : 0.004 0.036 481 Dihedral : 5.773 54.802 401 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.40 % Allowed : 27.89 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.45), residues: 378 helix: 1.13 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.74 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.021 0.001 PHE A 348 TYR 0.011 0.001 TYR A 422 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.254 Fit side-chains REVERT: A 166 PHE cc_start: 0.7540 (m-80) cc_final: 0.7215 (m-80) REVERT: A 189 ARG cc_start: 0.8349 (mmt180) cc_final: 0.8121 (mmt180) REVERT: A 204 MET cc_start: 0.8715 (mmt) cc_final: 0.8377 (mmt) REVERT: A 230 MET cc_start: 0.7417 (ttm) cc_final: 0.7086 (ttm) REVERT: A 286 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 353 HIS cc_start: 0.8612 (t-170) cc_final: 0.8068 (t-170) REVERT: A 453 MET cc_start: 0.8940 (mmm) cc_final: 0.8698 (mmm) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.1037 time to fit residues: 13.1475 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2867 Z= 0.238 Angle : 0.709 9.807 3907 Z= 0.336 Chirality : 0.043 0.143 477 Planarity : 0.004 0.037 481 Dihedral : 5.686 48.433 401 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.38 % Allowed : 29.59 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.45), residues: 378 helix: 1.23 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.98 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.023 0.002 PHE A 463 TYR 0.012 0.001 TYR A 422 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 166 PHE cc_start: 0.7496 (m-80) cc_final: 0.7188 (m-80) REVERT: A 189 ARG cc_start: 0.8398 (mmt180) cc_final: 0.8144 (mmt180) REVERT: A 204 MET cc_start: 0.8756 (mmt) cc_final: 0.8473 (mmt) REVERT: A 230 MET cc_start: 0.7453 (ttm) cc_final: 0.7121 (ttm) REVERT: A 286 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 353 HIS cc_start: 0.8616 (t-170) cc_final: 0.8081 (t-170) REVERT: A 453 MET cc_start: 0.9015 (mmm) cc_final: 0.8803 (mmm) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.0971 time to fit residues: 12.4754 Evaluate side-chains 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2867 Z= 0.211 Angle : 0.701 9.171 3907 Z= 0.332 Chirality : 0.042 0.145 477 Planarity : 0.004 0.038 481 Dihedral : 5.706 47.138 401 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.06 % Allowed : 28.91 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.45), residues: 378 helix: 1.16 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.72 (0.78), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.033 0.002 PHE A 463 TYR 0.010 0.001 TYR A 422 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.287 Fit side-chains REVERT: A 166 PHE cc_start: 0.7464 (m-80) cc_final: 0.7209 (m-80) REVERT: A 189 ARG cc_start: 0.8397 (mmt180) cc_final: 0.8125 (mmt180) REVERT: A 204 MET cc_start: 0.8805 (mmt) cc_final: 0.8481 (mmt) REVERT: A 230 MET cc_start: 0.7448 (ttm) cc_final: 0.7136 (ttm) REVERT: A 286 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8325 (p) REVERT: A 353 HIS cc_start: 0.8616 (t-170) cc_final: 0.8095 (t-170) REVERT: A 406 MET cc_start: 0.8179 (mmm) cc_final: 0.7924 (mtp) REVERT: A 453 MET cc_start: 0.9026 (mmm) cc_final: 0.8823 (mmm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.0890 time to fit residues: 11.5196 Evaluate side-chains 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2867 Z= 0.199 Angle : 0.725 10.924 3907 Z= 0.339 Chirality : 0.043 0.190 477 Planarity : 0.004 0.038 481 Dihedral : 5.848 49.159 401 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.38 % Allowed : 30.61 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.45), residues: 378 helix: 1.13 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.71 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.027 0.002 PHE A 463 TYR 0.011 0.001 TYR A 422 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.288 Fit side-chains REVERT: A 166 PHE cc_start: 0.7566 (m-80) cc_final: 0.7345 (m-80) REVERT: A 189 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8046 (mmt180) REVERT: A 204 MET cc_start: 0.8801 (mmt) cc_final: 0.8488 (mmt) REVERT: A 230 MET cc_start: 0.7347 (ttm) cc_final: 0.7066 (ttm) REVERT: A 286 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 335 LEU cc_start: 0.8968 (tp) cc_final: 0.8619 (tt) REVERT: A 353 HIS cc_start: 0.8619 (t-170) cc_final: 0.8111 (t-170) REVERT: A 402 MET cc_start: 0.8475 (tpp) cc_final: 0.8237 (tpp) REVERT: A 406 MET cc_start: 0.8159 (mmm) cc_final: 0.7901 (mtp) outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.1056 time to fit residues: 13.6580 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2867 Z= 0.193 Angle : 0.719 10.134 3907 Z= 0.337 Chirality : 0.043 0.173 477 Planarity : 0.004 0.038 481 Dihedral : 5.961 50.941 401 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.38 % Allowed : 31.97 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.45), residues: 378 helix: 1.07 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.76 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.025 0.002 PHE A 463 TYR 0.010 0.001 TYR A 422 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.306 Fit side-chains REVERT: A 166 PHE cc_start: 0.7591 (m-80) cc_final: 0.7391 (m-80) REVERT: A 204 MET cc_start: 0.8796 (mmt) cc_final: 0.8555 (mmt) REVERT: A 221 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: A 230 MET cc_start: 0.7358 (ttm) cc_final: 0.7095 (ttm) REVERT: A 286 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 353 HIS cc_start: 0.8613 (t-170) cc_final: 0.8111 (t-170) REVERT: A 402 MET cc_start: 0.8566 (tpp) cc_final: 0.8314 (tpp) REVERT: A 406 MET cc_start: 0.8141 (mmm) cc_final: 0.7893 (mtp) outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.0995 time to fit residues: 13.0168 Evaluate side-chains 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7383 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2867 Z= 0.234 Angle : 0.753 10.383 3907 Z= 0.358 Chirality : 0.045 0.173 477 Planarity : 0.004 0.038 481 Dihedral : 6.106 53.462 401 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.72 % Allowed : 30.61 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.44), residues: 378 helix: 1.09 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -1.97 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.029 0.002 PHE A 463 TYR 0.011 0.001 TYR A 422 ARG 0.007 0.001 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.281 Fit side-chains REVERT: A 189 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8095 (mmm-85) REVERT: A 204 MET cc_start: 0.8812 (mmt) cc_final: 0.8492 (mmt) REVERT: A 221 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: A 230 MET cc_start: 0.7358 (ttm) cc_final: 0.7096 (ttm) REVERT: A 286 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 353 HIS cc_start: 0.8622 (t-170) cc_final: 0.8133 (t-170) REVERT: A 402 MET cc_start: 0.8571 (tpp) cc_final: 0.8319 (tpp) REVERT: A 406 MET cc_start: 0.8193 (mmm) cc_final: 0.7910 (mtp) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.0992 time to fit residues: 12.6415 Evaluate side-chains 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130978 restraints weight = 4502.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134987 restraints weight = 2255.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137771 restraints weight = 1398.009| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2867 Z= 0.256 Angle : 0.755 10.282 3907 Z= 0.361 Chirality : 0.045 0.173 477 Planarity : 0.005 0.038 481 Dihedral : 6.283 55.847 401 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 30.27 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.44), residues: 378 helix: 1.04 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -1.85 (0.72), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.029 0.002 PHE A 463 TYR 0.013 0.001 TYR A 422 ARG 0.007 0.001 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.33 seconds wall clock time: 21 minutes 43.22 seconds (1303.22 seconds total)