Starting phenix.real_space_refine on Mon Jun 24 14:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/06_2024/8wlm_37624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/06_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_37624/06_2024/8wlm_37624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/06_2024/8wlm_37624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/06_2024/8wlm_37624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/06_2024/8wlm_37624_updated.pdb" } 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-5370/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: 2.25, per 1000 atoms: 0.80 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: 1.04 Conformation dependent library (CDL) restraints added in 609.8 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... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 83.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 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 133 through 155 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 177 removed outlier: 3.655A pdb=" N ILE A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 214 through 245 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 Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 322 removed outlier: 3.695A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 4.027A pdb=" N MET A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 355 removed outlier: 4.528A pdb=" N GLY A 331 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 3.518A pdb=" N GLY A 344 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 349 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 352 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 353 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 382 through 413 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 419 through 446 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 449 through 471 Proline residue: A 465 - end of helix removed outlier: 4.499A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 579 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: 0.70 Time building geometry restraints manager: 1.15 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: 241 2.74 - 3.28: 3138 3.28 - 3.82: 4835 3.82 - 4.36: 5284 4.36 - 4.90: 9302 Nonbonded interactions: 22800 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 22795 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: 0.010 Normalize map: mean=0, sd=1: 0.460 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: 0.000 Extract box with map and model: 2.300 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- 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= 0.290 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 : 0.295 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: 0.1215 time to fit residues: 15.9863 Evaluate side-chains 93 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.9980 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: 0.7980 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2867 Z= 0.221 Angle : 0.671 7.136 3907 Z= 0.328 Chirality : 0.042 0.133 477 Planarity : 0.005 0.040 481 Dihedral : 6.471 65.355 401 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 17.35 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.44), residues: 378 helix: 0.97 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.70 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.013 0.002 PHE A 348 TYR 0.017 0.001 TYR A 422 ARG 0.006 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 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.291 Fit side-chains REVERT: A 166 PHE cc_start: 0.7582 (m-80) cc_final: 0.7225 (m-80) REVERT: A 198 CYS cc_start: 0.8351 (p) cc_final: 0.8141 (p) REVERT: A 204 MET cc_start: 0.8716 (mmt) cc_final: 0.8464 (mmt) REVERT: A 230 MET cc_start: 0.7467 (ttm) cc_final: 0.7130 (ttm) REVERT: A 286 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 353 HIS cc_start: 0.8435 (t-170) cc_final: 0.7968 (t-170) REVERT: A 355 MET cc_start: 0.8346 (tmm) cc_final: 0.7770 (tmm) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1043 time to fit residues: 13.0582 Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 0.3980 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7336 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2867 Z= 0.194 Angle : 0.654 7.984 3907 Z= 0.314 Chirality : 0.041 0.123 477 Planarity : 0.004 0.036 481 Dihedral : 6.072 60.893 401 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.40 % Allowed : 19.39 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.44), residues: 378 helix: 1.05 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -1.45 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.001 PHE A 463 TYR 0.009 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 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.302 Fit side-chains REVERT: A 166 PHE cc_start: 0.7545 (m-80) cc_final: 0.7213 (m-80) REVERT: A 204 MET cc_start: 0.8703 (mmt) cc_final: 0.8417 (mmt) REVERT: A 211 TYR cc_start: 0.5992 (m-10) cc_final: 0.5523 (m-10) REVERT: A 230 MET cc_start: 0.7457 (ttm) cc_final: 0.7104 (ttm) REVERT: A 286 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 353 HIS cc_start: 0.8423 (t-170) cc_final: 0.7968 (t-170) REVERT: A 355 MET cc_start: 0.8344 (tmm) cc_final: 0.7818 (tmm) REVERT: A 468 PHE cc_start: 0.8402 (t80) cc_final: 0.8035 (t80) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.1055 time to fit residues: 13.0709 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 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** ** 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: 0.7363 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2867 Z= 0.212 Angle : 0.657 8.343 3907 Z= 0.313 Chirality : 0.042 0.120 477 Planarity : 0.004 0.036 481 Dihedral : 5.908 58.655 401 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.06 % Allowed : 23.13 % Favored : 73.81 % 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: 0.96 (0.44), residues: 378 helix: 1.16 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -1.57 (0.75), 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 0.013 0.001 PHE A 377 TYR 0.009 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 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.294 Fit side-chains REVERT: A 166 PHE cc_start: 0.7497 (m-80) cc_final: 0.7198 (m-80) REVERT: A 204 MET cc_start: 0.8724 (mmt) cc_final: 0.8447 (mmt) REVERT: A 211 TYR cc_start: 0.6081 (m-10) cc_final: 0.5682 (m-10) REVERT: A 230 MET cc_start: 0.7501 (ttm) cc_final: 0.7154 (ttm) REVERT: A 286 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 353 HIS cc_start: 0.8436 (t-170) cc_final: 0.7978 (t-170) REVERT: A 418 TYR cc_start: 0.8126 (m-80) cc_final: 0.7854 (m-80) REVERT: A 453 MET cc_start: 0.8857 (mmm) cc_final: 0.8626 (mmm) outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.1054 time to fit residues: 13.0815 Evaluate side-chains 95 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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: 0.7369 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2867 Z= 0.213 Angle : 0.664 8.517 3907 Z= 0.316 Chirality : 0.042 0.145 477 Planarity : 0.004 0.036 481 Dihedral : 5.763 54.187 401 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.40 % Allowed : 25.51 % Favored : 71.09 % 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: 0.96 (0.45), residues: 378 helix: 1.14 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.44 (0.77), residues: 69 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 0.018 0.001 PHE A 463 TYR 0.012 0.001 TYR A 341 ARG 0.007 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 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.291 Fit side-chains REVERT: A 166 PHE cc_start: 0.7448 (m-80) cc_final: 0.7148 (m-80) REVERT: A 204 MET cc_start: 0.8738 (mmt) cc_final: 0.8448 (mmt) REVERT: A 211 TYR cc_start: 0.6087 (m-10) cc_final: 0.5686 (m-10) REVERT: A 230 MET cc_start: 0.7424 (ttm) cc_final: 0.7114 (ttm) REVERT: A 286 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 353 HIS cc_start: 0.8437 (t-170) cc_final: 0.7992 (t-170) REVERT: A 418 TYR cc_start: 0.8180 (m-80) cc_final: 0.7930 (m-80) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.1013 time to fit residues: 12.3908 Evaluate side-chains 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 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** ** 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: 0.7377 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2867 Z= 0.219 Angle : 0.682 9.787 3907 Z= 0.320 Chirality : 0.042 0.124 477 Planarity : 0.004 0.036 481 Dihedral : 5.718 52.538 401 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.06 % Allowed : 26.87 % Favored : 70.07 % 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 (0.45), residues: 378 helix: 1.17 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -1.52 (0.76), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.017 0.001 PHE A 463 TYR 0.010 0.001 TYR A 422 ARG 0.005 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 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.267 Fit side-chains REVERT: A 166 PHE cc_start: 0.7405 (m-80) cc_final: 0.7187 (m-80) REVERT: A 189 ARG cc_start: 0.8323 (mmt180) cc_final: 0.8046 (mmt180) REVERT: A 211 TYR cc_start: 0.6116 (m-10) cc_final: 0.5711 (m-10) REVERT: A 230 MET cc_start: 0.7438 (ttm) cc_final: 0.7129 (ttm) REVERT: A 286 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 353 HIS cc_start: 0.8431 (t-170) cc_final: 0.7996 (t-170) REVERT: A 418 TYR cc_start: 0.8222 (m-80) cc_final: 0.7953 (m-80) outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.1152 time to fit residues: 13.9336 Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7387 moved from start: 0.2582 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= 0.222 Angle : 0.687 8.921 3907 Z= 0.320 Chirality : 0.041 0.127 477 Planarity : 0.004 0.037 481 Dihedral : 5.633 46.146 401 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.72 % Allowed : 27.55 % Favored : 69.73 % 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: 1.02 (0.44), residues: 378 helix: 1.19 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -1.49 (0.77), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.001 PHE A 463 TYR 0.008 0.001 TYR A 422 ARG 0.005 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 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.278 Fit side-chains REVERT: A 166 PHE cc_start: 0.7400 (m-80) cc_final: 0.7196 (m-80) REVERT: A 189 ARG cc_start: 0.8332 (mmt180) cc_final: 0.8052 (mmt180) REVERT: A 211 TYR cc_start: 0.6252 (m-10) cc_final: 0.5864 (m-10) REVERT: A 230 MET cc_start: 0.7455 (ttm) cc_final: 0.7141 (ttm) REVERT: A 286 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8305 (p) REVERT: A 319 MET cc_start: 0.8411 (mtp) cc_final: 0.8163 (mtm) REVERT: A 341 TYR cc_start: 0.8008 (t80) cc_final: 0.7747 (t80) REVERT: A 353 HIS cc_start: 0.8441 (t-170) cc_final: 0.8011 (t-170) REVERT: A 365 MET cc_start: 0.7806 (mmm) cc_final: 0.7592 (mmm) REVERT: A 418 TYR cc_start: 0.8258 (m-80) cc_final: 0.8037 (m-80) outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 0.1148 time to fit residues: 14.6884 Evaluate side-chains 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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: 0.5980 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7385 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2867 Z= 0.226 Angle : 0.692 9.098 3907 Z= 0.329 Chirality : 0.043 0.210 477 Planarity : 0.004 0.037 481 Dihedral : 5.711 46.450 401 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.06 % Allowed : 27.21 % Favored : 69.73 % 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: 1.02 (0.44), residues: 378 helix: 1.27 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -1.69 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.030 0.002 PHE A 463 TYR 0.008 0.001 TYR A 422 ARG 0.005 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 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.298 Fit side-chains REVERT: A 189 ARG cc_start: 0.8356 (mmt180) cc_final: 0.8073 (mmt180) REVERT: A 211 TYR cc_start: 0.6303 (m-10) cc_final: 0.5903 (m-10) REVERT: A 230 MET cc_start: 0.7458 (ttm) cc_final: 0.7149 (ttm) REVERT: A 286 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8309 (p) REVERT: A 341 TYR cc_start: 0.8019 (t80) cc_final: 0.7755 (t80) REVERT: A 353 HIS cc_start: 0.8422 (t-170) cc_final: 0.7992 (t-170) REVERT: A 365 MET cc_start: 0.7832 (mmm) cc_final: 0.7627 (mmm) REVERT: A 418 TYR cc_start: 0.8268 (m-80) cc_final: 0.8056 (m-80) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.1142 time to fit residues: 14.1028 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.0020 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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: 0.7350 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2867 Z= 0.193 Angle : 0.668 9.612 3907 Z= 0.313 Chirality : 0.041 0.127 477 Planarity : 0.004 0.038 481 Dihedral : 5.681 48.860 401 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 26.53 % 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: 1.05 (0.45), residues: 378 helix: 1.17 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -1.29 (0.80), 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 0.024 0.001 PHE A 463 TYR 0.008 0.001 TYR A 422 ARG 0.005 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 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.307 Fit side-chains REVERT: A 189 ARG cc_start: 0.8255 (mmt180) cc_final: 0.8012 (mmt180) REVERT: A 211 TYR cc_start: 0.6189 (m-10) cc_final: 0.5882 (m-10) REVERT: A 230 MET cc_start: 0.7426 (ttm) cc_final: 0.7140 (ttm) REVERT: A 286 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 341 TYR cc_start: 0.7913 (t80) cc_final: 0.7465 (t80) REVERT: A 353 HIS cc_start: 0.8371 (t-170) cc_final: 0.7902 (t-170) REVERT: A 365 MET cc_start: 0.7791 (mmm) cc_final: 0.7583 (mmm) REVERT: A 402 MET cc_start: 0.8517 (tpp) cc_final: 0.8302 (tpp) REVERT: A 406 MET cc_start: 0.8124 (mmm) cc_final: 0.7872 (mtp) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.1136 time to fit residues: 14.5150 Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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: 0.7369 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2867 Z= 0.217 Angle : 0.696 9.243 3907 Z= 0.328 Chirality : 0.043 0.178 477 Planarity : 0.004 0.037 481 Dihedral : 5.805 50.235 401 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.38 % Allowed : 27.89 % Favored : 69.73 % 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: 1.09 (0.44), residues: 378 helix: 1.26 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -1.45 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.027 0.002 PHE A 468 TYR 0.008 0.001 TYR A 422 ARG 0.004 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 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.298 Fit side-chains REVERT: A 189 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8077 (mmt180) REVERT: A 211 TYR cc_start: 0.6230 (m-10) cc_final: 0.5901 (m-10) REVERT: A 230 MET cc_start: 0.7430 (ttm) cc_final: 0.7158 (ttm) REVERT: A 286 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 341 TYR cc_start: 0.7933 (t80) cc_final: 0.7443 (t80) REVERT: A 353 HIS cc_start: 0.8393 (t-170) cc_final: 0.7982 (t-170) REVERT: A 365 MET cc_start: 0.7822 (mmm) cc_final: 0.7484 (mmm) REVERT: A 406 MET cc_start: 0.8169 (mmm) cc_final: 0.7883 (mtp) REVERT: A 460 ASP cc_start: 0.8177 (t0) cc_final: 0.7766 (t0) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.1157 time to fit residues: 13.5561 Evaluate side-chains 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134761 restraints weight = 4354.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138624 restraints weight = 2292.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141376 restraints weight = 1464.667| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2897 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= 0.197 Angle : 0.685 9.664 3907 Z= 0.323 Chirality : 0.042 0.147 477 Planarity : 0.004 0.038 481 Dihedral : 5.814 50.450 401 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.72 % Allowed : 27.21 % Favored : 70.07 % 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: 1.14 (0.45), residues: 378 helix: 1.27 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.34 (0.81), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.022 0.001 PHE A 463 TYR 0.014 0.001 TYR A 182 ARG 0.005 0.001 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.06 seconds wall clock time: 19 minutes 11.39 seconds (1151.39 seconds total)