Starting phenix.real_space_refine on Fri Aug 2 13:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/08_2024/8wlm_37624.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/08_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_37624/08_2024/8wlm_37624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/08_2024/8wlm_37624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/08_2024/8wlm_37624.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlm_37624/08_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-5409/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: 2.28, per 1000 atoms: 0.81 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: 1.03 Conformation dependent library (CDL) restraints added in 660.4 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: 0.26 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: 0.80 Time building geometry restraints manager: 1.11 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 3.040 nonbonded pdb=" OE2 GLU A 215 " pdb=" ND1 HIS A 353 " model vdw 2.424 3.120 nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.426 3.120 nonbonded pdb=" OD2 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.464 3.120 nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.501 3.040 ... (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: 0.440 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- 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 : 0.303 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: 0.1224 time to fit residues: 16.0770 Evaluate side-chains 93 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.7331 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2867 Z= 0.207 Angle : 0.685 7.805 3907 Z= 0.337 Chirality : 0.042 0.138 477 Planarity : 0.005 0.034 481 Dihedral : 6.402 63.195 401 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 17.01 % Favored : 81.29 % 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: 0.76 (0.44), residues: 378 helix: 1.06 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.08 (0.68), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 353 PHE 0.017 0.001 PHE A 348 TYR 0.017 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 104 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.295 Fit side-chains REVERT: A 166 PHE cc_start: 0.7589 (m-80) cc_final: 0.7233 (m-80) REVERT: A 204 MET cc_start: 0.8710 (mmt) cc_final: 0.8446 (mmt) REVERT: A 230 MET cc_start: 0.7451 (ttm) cc_final: 0.7127 (ttm) REVERT: A 286 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 353 HIS cc_start: 0.8605 (t-170) cc_final: 0.8184 (t-170) outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 0.0942 time to fit residues: 12.2944 Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 214 ASP 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 3 optimal weight: 0.0000 overall best weight: 0.5544 ------------------------------------------------------------------------------- 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: 0.7339 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2867 Z= 0.195 Angle : 0.679 8.113 3907 Z= 0.331 Chirality : 0.042 0.137 477 Planarity : 0.004 0.036 481 Dihedral : 6.045 58.634 401 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 21.09 % Favored : 75.85 % 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: 0.92 (0.44), residues: 378 helix: 1.15 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.93 (0.70), 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 0.019 0.001 PHE A 348 TYR 0.010 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 104 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.308 Fit side-chains REVERT: A 166 PHE cc_start: 0.7486 (m-80) cc_final: 0.7161 (m-80) REVERT: A 204 MET cc_start: 0.8710 (mmt) cc_final: 0.8420 (mmt) REVERT: A 230 MET cc_start: 0.7411 (ttm) cc_final: 0.7080 (ttm) REVERT: A 335 LEU cc_start: 0.8872 (tp) cc_final: 0.8638 (tp) REVERT: A 353 HIS cc_start: 0.8603 (t-170) cc_final: 0.8306 (t70) REVERT: A 468 PHE cc_start: 0.8430 (t80) cc_final: 0.8029 (t80) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.1179 time to fit residues: 15.1487 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain A residue 286 THR 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: 0.8980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7347 moved from start: 0.2015 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= 0.203 Angle : 0.681 8.355 3907 Z= 0.329 Chirality : 0.042 0.140 477 Planarity : 0.004 0.035 481 Dihedral : 5.912 55.992 401 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.40 % Allowed : 23.47 % Favored : 73.13 % 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 (0.44), residues: 378 helix: 1.19 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.86 (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 0.019 0.001 PHE A 348 TYR 0.010 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 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.316 Fit side-chains REVERT: A 166 PHE cc_start: 0.7468 (m-80) cc_final: 0.7211 (m-80) REVERT: A 204 MET cc_start: 0.8719 (mmt) cc_final: 0.8404 (mmt) REVERT: A 230 MET cc_start: 0.7414 (ttm) cc_final: 0.7111 (ttm) REVERT: A 346 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8291 (m110) REVERT: A 353 HIS cc_start: 0.8606 (t-170) cc_final: 0.8337 (t70) REVERT: A 355 MET cc_start: 0.8166 (tmm) cc_final: 0.7688 (tmm) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1006 time to fit residues: 13.1186 Evaluate side-chains 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 346 ASN 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: 0.0050 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.2972 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2867 Z= 0.188 Angle : 0.680 9.072 3907 Z= 0.325 Chirality : 0.043 0.174 477 Planarity : 0.004 0.035 481 Dihedral : 5.859 55.252 401 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 1.07 (0.45), residues: 378 helix: 1.25 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.68 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.022 0.001 PHE A 348 TYR 0.009 0.001 TYR A 422 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 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.298 Fit side-chains REVERT: A 166 PHE cc_start: 0.7463 (m-80) cc_final: 0.7241 (m-80) REVERT: A 204 MET cc_start: 0.8644 (mmt) cc_final: 0.8356 (mmt) REVERT: A 221 MET cc_start: 0.8612 (ttm) cc_final: 0.8347 (ttp) REVERT: A 230 MET cc_start: 0.7319 (ttm) cc_final: 0.7026 (ttm) REVERT: A 286 THR cc_start: 0.8579 (m) cc_final: 0.8228 (p) REVERT: A 346 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8160 (m110) REVERT: A 355 MET cc_start: 0.8121 (tmm) cc_final: 0.7618 (tmm) REVERT: A 365 MET cc_start: 0.7735 (mmm) cc_final: 0.7530 (mmm) REVERT: A 453 MET cc_start: 0.8949 (mmm) cc_final: 0.8660 (mmm) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.1004 time to fit residues: 12.9454 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 214 ASP Chi-restraints excluded: chain A residue 346 ASN 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: 0.8980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2473 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= 0.219 Angle : 0.690 8.502 3907 Z= 0.331 Chirality : 0.043 0.141 477 Planarity : 0.004 0.036 481 Dihedral : 5.866 54.840 401 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 1.13 (0.45), residues: 378 helix: 1.30 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.72 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 353 PHE 0.023 0.002 PHE A 463 TYR 0.011 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 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.273 Fit side-chains REVERT: A 23 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8493 (mt) REVERT: A 166 PHE cc_start: 0.7477 (m-80) cc_final: 0.7248 (m-80) REVERT: A 189 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8061 (mmt180) REVERT: A 204 MET cc_start: 0.8670 (mmt) cc_final: 0.8364 (mmt) REVERT: A 230 MET cc_start: 0.7416 (ttm) cc_final: 0.7135 (ttm) REVERT: A 286 THR cc_start: 0.8635 (m) cc_final: 0.8284 (p) REVERT: A 346 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7976 (m110) REVERT: A 355 MET cc_start: 0.8193 (tmm) cc_final: 0.7744 (tmm) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 0.0966 time to fit residues: 12.2097 Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 214 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 346 ASN 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: 0.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 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 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2588 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= 0.216 Angle : 0.692 8.839 3907 Z= 0.332 Chirality : 0.043 0.142 477 Planarity : 0.004 0.037 481 Dihedral : 5.774 47.866 401 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 1.10 (0.45), residues: 378 helix: 1.26 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.82 (0.75), 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 414 PHE 0.020 0.002 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.007 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 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.321 Fit side-chains REVERT: A 23 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (mt) REVERT: A 166 PHE cc_start: 0.7575 (m-80) cc_final: 0.7333 (m-80) REVERT: A 189 ARG cc_start: 0.8351 (mmt180) cc_final: 0.8098 (mmt180) REVERT: A 204 MET cc_start: 0.8700 (mmt) cc_final: 0.8392 (mmt) REVERT: A 230 MET cc_start: 0.7445 (ttm) cc_final: 0.7146 (ttm) REVERT: A 286 THR cc_start: 0.8641 (m) cc_final: 0.8299 (p) REVERT: A 346 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7811 (m110) REVERT: A 355 MET cc_start: 0.8266 (tmm) cc_final: 0.7675 (tmm) REVERT: A 406 MET cc_start: 0.8156 (mmm) cc_final: 0.7889 (mtp) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.1018 time to fit residues: 12.5877 Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 214 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 346 ASN 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: 0.4980 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2639 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= 0.207 Angle : 0.702 8.769 3907 Z= 0.336 Chirality : 0.043 0.173 477 Planarity : 0.004 0.037 481 Dihedral : 5.814 48.809 401 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 1.20 (0.45), residues: 378 helix: 1.32 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.60 (0.76), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.022 0.002 PHE A 348 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 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.310 Fit side-chains REVERT: A 166 PHE cc_start: 0.7677 (m-80) cc_final: 0.7442 (m-80) REVERT: A 189 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8011 (mmt180) REVERT: A 204 MET cc_start: 0.8704 (mmt) cc_final: 0.8490 (mmt) REVERT: A 230 MET cc_start: 0.7388 (ttm) cc_final: 0.7112 (ttm) REVERT: A 286 THR cc_start: 0.8634 (m) cc_final: 0.8291 (p) REVERT: A 346 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (m110) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.0999 time to fit residues: 12.6634 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 295 LEU Chi-restraints excluded: chain A residue 346 ASN 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: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2744 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 : 0.694 9.066 3907 Z= 0.332 Chirality : 0.042 0.143 477 Planarity : 0.004 0.037 481 Dihedral : 5.939 50.996 401 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.06 % Allowed : 26.19 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.45), residues: 378 helix: 1.25 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.75 (0.76), residues: 64 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 0.037 0.002 PHE A 463 TYR 0.010 0.001 TYR A 422 ARG 0.006 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 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.297 Fit side-chains REVERT: A 166 PHE cc_start: 0.7618 (m-80) cc_final: 0.7356 (m-80) REVERT: A 189 ARG cc_start: 0.8341 (mmt180) cc_final: 0.8094 (mmt180) REVERT: A 204 MET cc_start: 0.8760 (mmt) cc_final: 0.8468 (mmt) REVERT: A 230 MET cc_start: 0.7378 (ttm) cc_final: 0.7105 (ttm) REVERT: A 286 THR cc_start: 0.8639 (m) cc_final: 0.8295 (p) REVERT: A 341 TYR cc_start: 0.8514 (t80) cc_final: 0.8249 (t80) REVERT: A 346 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7877 (m110) REVERT: A 355 MET cc_start: 0.8279 (tmm) cc_final: 0.7760 (tmm) REVERT: A 365 MET cc_start: 0.7705 (mmm) cc_final: 0.7365 (mmm) REVERT: A 406 MET cc_start: 0.8124 (mmm) cc_final: 0.7897 (mtp) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.1032 time to fit residues: 12.7616 Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 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 214 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 346 ASN 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: 0.0470 chunk 32 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.3464 ------------------------------------------------------------------------------- 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: 0.7322 moved from start: 0.2803 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= 0.183 Angle : 0.710 9.657 3907 Z= 0.334 Chirality : 0.042 0.143 477 Planarity : 0.004 0.038 481 Dihedral : 5.949 51.900 401 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 1.12 (0.45), residues: 378 helix: 1.22 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.50 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.034 0.002 PHE A 463 TYR 0.013 0.001 TYR A 422 ARG 0.006 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 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.300 Fit side-chains REVERT: A 189 ARG cc_start: 0.8319 (mmt180) cc_final: 0.8060 (mmt180) REVERT: A 204 MET cc_start: 0.8752 (mmt) cc_final: 0.8487 (mmt) REVERT: A 230 MET cc_start: 0.7324 (ttm) cc_final: 0.7053 (ttm) REVERT: A 286 THR cc_start: 0.8618 (m) cc_final: 0.8273 (p) REVERT: A 306 MET cc_start: 0.8247 (tpp) cc_final: 0.7604 (tpp) REVERT: A 341 TYR cc_start: 0.8480 (t80) cc_final: 0.8113 (t80) REVERT: A 346 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7745 (m110) REVERT: A 355 MET cc_start: 0.8271 (tmm) cc_final: 0.7823 (tmm) REVERT: A 402 MET cc_start: 0.8575 (tpp) cc_final: 0.8278 (tpp) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1023 time to fit residues: 12.4399 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 346 ASN 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: 0.6980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 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 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134776 restraints weight = 4529.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138964 restraints weight = 2180.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141548 restraints weight = 1314.055| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2867 Z= 0.217 Angle : 0.697 9.184 3907 Z= 0.332 Chirality : 0.043 0.143 477 Planarity : 0.004 0.037 481 Dihedral : 6.020 52.282 401 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.38 % Allowed : 28.57 % Favored : 69.05 % 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 (0.44), residues: 378 helix: 1.15 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.66 (0.79), residues: 61 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 0.038 0.002 PHE A 463 TYR 0.012 0.001 TYR A 422 ARG 0.006 0.001 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1011.21 seconds wall clock time: 18 minutes 50.13 seconds (1130.13 seconds total)