Starting phenix.real_space_refine on Fri Apr 5 14:58:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/04_2024/8jts_36651_updated.pdb" } resolution = 4.14 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= 0.002 sd= 0.079 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 23 5.16 5 C 2190 2.51 5 N 534 2.21 5 O 583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3321 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 157 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.68 Number of scatterers: 3330 At special positions: 0 Unit cell: (94.1775, 58.455, 67.115, 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 23 16.00 O 583 8.00 N 534 7.00 C 2190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 644.4 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 0 sheets defined 70.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.638A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 36 No H-bonds generated for 'chain 'A' and resid 33 through 36' Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 145 through 165 removed outlier: 3.707A pdb=" N LEU A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 200 through 227 Processing helix chain 'A' and resid 233 through 257 Processing helix chain 'A' and resid 261 through 278 removed outlier: 3.668A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.896A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 377 through 396 removed outlier: 3.657A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 401 through 422 Proline residue: A 405 - end of helix removed outlier: 3.865A pdb=" N MET A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 4.146A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.081A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 Proline residue: A 481 - end of helix removed outlier: 3.888A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'A' and resid 527 through 530 No H-bonds generated for 'chain 'A' and resid 527 through 530' 207 hydrogen bonds defined for protein. 570 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: 0.90 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 533 1.30 - 1.43: 891 1.43 - 1.56: 1950 1.56 - 1.69: 0 1.69 - 1.82: 35 Bond restraints: 3409 Sorted by residual: bond pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.27e-02 6.20e+03 7.52e+01 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.447 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N ARG A 439 " pdb=" CA ARG A 439 " ideal model delta sigma weight residual 1.459 1.363 0.095 1.24e-02 6.50e+03 5.90e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.245 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 1.530 1.432 0.098 1.57e-02 4.06e+03 3.91e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.15: 76 105.15 - 112.36: 1743 112.36 - 119.57: 1130 119.57 - 126.78: 1665 126.78 - 133.99: 62 Bond angle restraints: 4676 Sorted by residual: angle pdb=" N THR A 356 " pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 111.07 102.52 8.55 1.07e+00 8.73e-01 6.38e+01 angle pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta sigma weight residual 120.65 110.87 9.78 1.32e+00 5.74e-01 5.49e+01 angle pdb=" CA ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 116.92 124.94 -8.02 1.16e+00 7.43e-01 4.79e+01 angle pdb=" N GLN A 362 " pdb=" CA GLN A 362 " pdb=" C GLN A 362 " ideal model delta sigma weight residual 111.75 104.24 7.51 1.28e+00 6.10e-01 3.44e+01 angle pdb=" O ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 122.03 116.89 5.14 1.04e+00 9.25e-01 2.44e+01 ... (remaining 4671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1767 17.47 - 34.94: 148 34.94 - 52.41: 29 52.41 - 69.89: 7 69.89 - 87.36: 3 Dihedral angle restraints: 1954 sinusoidal: 634 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ILE A 442 " pdb=" C ILE A 442 " pdb=" N THR A 443 " pdb=" CA THR A 443 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA MET A 448 " pdb=" C MET A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 465 0.056 - 0.112: 92 0.112 - 0.168: 8 0.168 - 0.224: 2 0.224 - 0.280: 4 Chirality restraints: 571 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP A 357 " pdb=" N ASP A 357 " pdb=" C ASP A 357 " pdb=" CB ASP A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TYR A 361 " pdb=" N TYR A 361 " pdb=" C TYR A 361 " pdb=" CB TYR A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 568 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.070 2.00e-02 2.50e+03 4.80e-01 5.19e+03 pdb=" C03 MF8 A 601 " 0.458 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.216 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.227 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.055 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -1.078 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.514 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " -0.349 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.459 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C TYR A 361 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR A 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 743 2.78 - 3.31: 3509 3.31 - 3.84: 5627 3.84 - 4.37: 5769 4.37 - 4.90: 9814 Nonbonded interactions: 25462 Sorted by model distance: nonbonded pdb=" O GLY A 167 " pdb=" ND2 ASN A 463 " model vdw 2.249 2.520 nonbonded pdb=" OG SER A 424 " pdb=" OD1 ASP A 426 " model vdw 2.315 2.440 nonbonded pdb=" O GLY A 12 " pdb=" NE2 GLN A 18 " model vdw 2.327 2.520 nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.345 2.440 nonbonded pdb=" O VAL A 141 " pdb=" OG SER A 145 " model vdw 2.367 2.440 ... (remaining 25457 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: 0.320 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: 1.800 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 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 : 0.008 0.166 3409 Z= 0.574 Angle : 0.933 9.780 4676 Z= 0.539 Chirality : 0.049 0.280 571 Planarity : 0.021 0.480 582 Dihedral : 14.111 87.356 1104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 0.94 % Favored : 98.75 % 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: -0.32 (0.39), residues: 457 helix: 0.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.17 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.001 0.000 HIS A 260 PHE 0.021 0.002 PHE A 151 TYR 0.010 0.001 TYR A 256 ARG 0.006 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.356 Fit side-chains REVERT: A 137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 293 LYS cc_start: 0.8310 (mttm) cc_final: 0.8109 (mttm) REVERT: A 352 TYR cc_start: 0.5406 (m-80) cc_final: 0.5079 (m-80) REVERT: A 361 TYR cc_start: 0.8688 (t80) cc_final: 0.8330 (t80) REVERT: A 449 ILE cc_start: 0.8890 (tt) cc_final: 0.8569 (tt) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1161 time to fit residues: 14.0622 Evaluate side-chains 80 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 41 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3409 Z= 0.167 Angle : 0.575 7.091 4676 Z= 0.288 Chirality : 0.039 0.166 571 Planarity : 0.005 0.061 582 Dihedral : 4.295 19.114 479 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.40), residues: 457 helix: 0.74 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.13 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 288 HIS 0.000 0.000 HIS A 260 PHE 0.018 0.001 PHE A 41 TYR 0.009 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.378 Fit side-chains REVERT: A 137 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6626 (mm-30) REVERT: A 352 TYR cc_start: 0.5300 (m-80) cc_final: 0.5088 (m-80) REVERT: A 361 TYR cc_start: 0.8439 (t80) cc_final: 0.7979 (t80) REVERT: A 449 ILE cc_start: 0.8885 (tt) cc_final: 0.8526 (tt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1139 time to fit residues: 13.4563 Evaluate side-chains 77 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3409 Z= 0.166 Angle : 0.579 7.025 4676 Z= 0.284 Chirality : 0.039 0.164 571 Planarity : 0.005 0.059 582 Dihedral : 4.102 14.066 479 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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 (0.40), residues: 457 helix: 0.95 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.20 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.000 0.000 HIS A 260 PHE 0.012 0.001 PHE A 41 TYR 0.015 0.001 TYR A 361 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.290 Fit side-chains REVERT: A 137 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6676 (mm-30) REVERT: A 449 ILE cc_start: 0.8803 (tt) cc_final: 0.8553 (tt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1081 time to fit residues: 12.9362 Evaluate side-chains 76 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3409 Z= 0.174 Angle : 0.579 7.173 4676 Z= 0.287 Chirality : 0.040 0.194 571 Planarity : 0.005 0.060 582 Dihedral : 4.072 14.318 479 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 4.38 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.40), residues: 457 helix: 1.04 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.35 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 367 PHE 0.017 0.001 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.430 Fit side-chains REVERT: A 137 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 352 TYR cc_start: 0.5336 (m-80) cc_final: 0.5037 (m-80) REVERT: A 449 ILE cc_start: 0.8833 (tt) cc_final: 0.8554 (tt) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.0992 time to fit residues: 12.0385 Evaluate side-chains 77 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3409 Z= 0.173 Angle : 0.576 6.616 4676 Z= 0.287 Chirality : 0.039 0.184 571 Planarity : 0.005 0.060 582 Dihedral : 4.042 14.250 479 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 0.54 (0.40), residues: 457 helix: 1.02 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.39 (0.56), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.000 0.000 HIS A 367 PHE 0.021 0.001 PHE A 41 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.394 Fit side-chains REVERT: A 137 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6756 (mm-30) REVERT: A 287 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8336 (ttm-80) REVERT: A 449 ILE cc_start: 0.8853 (tt) cc_final: 0.8595 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1227 time to fit residues: 15.2811 Evaluate side-chains 79 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.190 Angle : 0.599 7.313 4676 Z= 0.299 Chirality : 0.040 0.176 571 Planarity : 0.005 0.058 582 Dihedral : 4.073 14.783 479 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 0.44 (0.40), residues: 457 helix: 0.92 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.35 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.020 0.002 PHE A 41 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.390 Fit side-chains REVERT: A 137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6774 (mm-30) REVERT: A 287 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8351 (ttm-80) REVERT: A 449 ILE cc_start: 0.8887 (tt) cc_final: 0.8611 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1078 time to fit residues: 14.1072 Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3409 Z= 0.156 Angle : 0.593 7.538 4676 Z= 0.286 Chirality : 0.039 0.230 571 Planarity : 0.005 0.057 582 Dihedral : 3.966 14.922 479 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 0.64 (0.40), residues: 457 helix: 1.05 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.21 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.017 0.001 PHE A 41 TYR 0.007 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.352 Fit side-chains REVERT: A 287 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8383 (ttm-80) REVERT: A 449 ILE cc_start: 0.8849 (tt) cc_final: 0.8555 (tt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1096 time to fit residues: 13.9408 Evaluate side-chains 78 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.202 Angle : 0.616 7.475 4676 Z= 0.309 Chirality : 0.041 0.225 571 Planarity : 0.005 0.058 582 Dihedral : 4.095 15.198 479 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.53 (0.40), residues: 457 helix: 0.91 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.09 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.000 0.000 HIS A 260 PHE 0.023 0.002 PHE A 41 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.303 Fit side-chains REVERT: A 137 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6640 (mm-30) REVERT: A 287 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8442 (ttm-80) REVERT: A 449 ILE cc_start: 0.8911 (tt) cc_final: 0.8613 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0974 time to fit residues: 12.7271 Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.178 Angle : 0.617 7.529 4676 Z= 0.302 Chirality : 0.040 0.221 571 Planarity : 0.005 0.058 582 Dihedral : 4.039 15.696 479 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 457 helix: 1.08 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.06 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 217 HIS 0.000 0.000 HIS A 260 PHE 0.015 0.001 PHE A 41 TYR 0.009 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.348 Fit side-chains REVERT: A 137 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6524 (mm-30) REVERT: A 287 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8477 (ttm-80) REVERT: A 449 ILE cc_start: 0.8877 (tt) cc_final: 0.8677 (tt) REVERT: A 478 ILE cc_start: 0.8909 (mt) cc_final: 0.8699 (mt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1048 time to fit residues: 13.2573 Evaluate side-chains 81 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3409 Z= 0.176 Angle : 0.635 8.711 4676 Z= 0.308 Chirality : 0.040 0.219 571 Planarity : 0.005 0.058 582 Dihedral : 4.016 16.395 479 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.40), residues: 457 helix: 1.10 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -0.96 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.000 0.000 HIS A 260 PHE 0.017 0.001 PHE A 227 TYR 0.009 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.351 Fit side-chains REVERT: A 449 ILE cc_start: 0.8947 (tt) cc_final: 0.8640 (tt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1023 time to fit residues: 12.3720 Evaluate side-chains 77 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 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 = 0.4397 r_free = 0.4397 target = 0.199232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175558 restraints weight = 4875.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.179624 restraints weight = 2815.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.182321 restraints weight = 1872.063| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3409 Z= 0.208 Angle : 0.651 8.238 4676 Z= 0.320 Chirality : 0.041 0.240 571 Planarity : 0.005 0.057 582 Dihedral : 4.117 16.579 479 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.73 (0.40), residues: 457 helix: 1.09 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.97 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.000 0.000 HIS A 367 PHE 0.018 0.002 PHE A 41 TYR 0.011 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.20 seconds wall clock time: 19 minutes 56.82 seconds (1196.82 seconds total)