Starting phenix.real_space_refine on Wed Mar 5 23:24:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgv_37233/03_2025/8kgv_37233.cif" } resolution = 3.2 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= 0.000 sd= 0.077 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 36 5.16 5 C 2673 2.51 5 N 652 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4056 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4042 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 29, 'TRANS': 503} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.75 Number of scatterers: 4056 At special positions: 0 Unit cell: (64.308, 89.472, 81.084, 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 36 16.00 O 695 8.00 N 652 7.00 C 2673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 478 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 510.2 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 73.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 4.084A pdb=" N ASN A 30 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 64 removed outlier: 5.081A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 removed outlier: 3.619A pdb=" N SER A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 116 removed outlier: 3.720A pdb=" N LEU A 100 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.566A pdb=" N PHE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.718A pdb=" N PHE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Proline residue: A 219 - end of helix removed outlier: 3.550A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.865A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 261 " --> pdb=" O TRP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 325 through 348 removed outlier: 4.187A pdb=" N PHE A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 360 through 390 removed outlier: 4.943A pdb=" N LEU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.912A pdb=" N ARG A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 402 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 removed outlier: 4.113A pdb=" N PHE A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 removed outlier: 4.501A pdb=" N CYS A 448 " --> pdb=" O CYS A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 448' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 514 through 531 Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.549A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 579 removed outlier: 4.002A pdb=" N ALA A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 629 removed outlier: 3.908A pdb=" N ASP A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.513A pdb=" N ALA A 502 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 583 through 585 removed outlier: 6.409A pdb=" N ASN A 584 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 592 " --> pdb=" O ASN A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 259 hydrogen bonds defined for protein. 765 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: 1.14 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1149 1.34 - 1.46: 975 1.46 - 1.58: 1986 1.58 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4161 Sorted by residual: bond pdb=" N TYR A 429 " pdb=" CA TYR A 429 " ideal model delta sigma weight residual 1.462 1.491 -0.030 9.50e-03 1.11e+04 9.80e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.93e+00 bond pdb=" N ILE A 397 " pdb=" CA ILE A 397 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.18e-02 7.18e+03 6.93e+00 bond pdb=" N LEU A 602 " pdb=" CA LEU A 602 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.70e+00 bond pdb=" N VAL A 413 " pdb=" CA VAL A 413 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.18e-02 7.18e+03 6.66e+00 ... (remaining 4156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 5494 2.15 - 4.31: 137 4.31 - 6.46: 25 6.46 - 8.61: 6 8.61 - 10.77: 1 Bond angle restraints: 5663 Sorted by residual: angle pdb=" N THR A 403 " pdb=" CA THR A 403 " pdb=" C THR A 403 " ideal model delta sigma weight residual 111.07 106.82 4.25 1.07e+00 8.73e-01 1.58e+01 angle pdb=" N PHE A 382 " pdb=" CA PHE A 382 " pdb=" C PHE A 382 " ideal model delta sigma weight residual 112.54 107.71 4.83 1.22e+00 6.72e-01 1.57e+01 angle pdb=" N PRO A 431 " pdb=" CA PRO A 431 " pdb=" CB PRO A 431 " ideal model delta sigma weight residual 103.00 98.90 4.10 1.10e+00 8.26e-01 1.39e+01 angle pdb=" N PRO A 430 " pdb=" CA PRO A 430 " pdb=" C PRO A 430 " ideal model delta sigma weight residual 110.70 106.31 4.39 1.22e+00 6.72e-01 1.30e+01 angle pdb=" CB MET A 611 " pdb=" CG MET A 611 " pdb=" SD MET A 611 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 ... (remaining 5658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 2194 16.57 - 33.13: 206 33.13 - 49.70: 47 49.70 - 66.26: 8 66.26 - 82.83: 2 Dihedral angle restraints: 2457 sinusoidal: 925 harmonic: 1532 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 507 " pdb=" CB CYS A 507 " ideal model delta sinusoidal sigma weight residual -86.00 -3.17 -82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 580 " pdb=" SG CYS A 580 " pdb=" SG CYS A 594 " pdb=" CB CYS A 594 " ideal model delta sinusoidal sigma weight residual -86.00 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -58.23 -27.77 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 2454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 552 0.066 - 0.132: 100 0.132 - 0.199: 8 0.199 - 0.265: 2 0.265 - 0.331: 2 Chirality restraints: 664 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 478 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE A 187 " pdb=" CA ILE A 187 " pdb=" CG1 ILE A 187 " pdb=" CG2 ILE A 187 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 661 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 468 " -0.051 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO A 469 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 605 " -0.251 9.50e-02 1.11e+02 1.13e-01 7.79e+00 pdb=" NE ARG A 605 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 605 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 605 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 605 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 430 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C PRO A 430 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO A 430 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 431 " 0.012 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1190 2.82 - 3.34: 4158 3.34 - 3.86: 6707 3.86 - 4.38: 7597 4.38 - 4.90: 13025 Nonbonded interactions: 32677 Sorted by model distance: nonbonded pdb=" OG SER A 340 " pdb=" OG SER A 568 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 194 " pdb=" O PRO A 279 " model vdw 2.389 3.040 nonbonded pdb=" NH1 ARG A 97 " pdb=" OG SER A 193 " model vdw 2.415 3.120 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.415 3.040 nonbonded pdb=" O SER A 532 " pdb=" OG SER A 532 " model vdw 2.422 3.040 ... (remaining 32672 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 individual isotropic 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: 0.670 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.130 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.005 0.048 4161 Z= 0.292 Angle : 0.802 10.766 5663 Z= 0.449 Chirality : 0.053 0.331 664 Planarity : 0.007 0.113 701 Dihedral : 13.393 67.287 1455 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.52 % Favored : 98.29 % Rotamer: Outliers : 0.23 % Allowed : 0.69 % Favored : 99.08 % 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: 0.35 (0.36), residues: 525 helix: 1.17 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.59 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 258 HIS 0.001 0.000 HIS A 96 PHE 0.025 0.001 PHE A 217 TYR 0.016 0.001 TYR A 429 ARG 0.003 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.471 Fit side-chains REVERT: A 324 MET cc_start: 0.7200 (mmp) cc_final: 0.6900 (mmp) REVERT: A 465 GLU cc_start: 0.8002 (mt-10) cc_final: 0.6800 (mp0) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1412 time to fit residues: 18.7824 Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.179339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140765 restraints weight = 5210.642| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.77 r_work: 0.3651 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4161 Z= 0.232 Angle : 0.627 7.475 5663 Z= 0.308 Chirality : 0.042 0.195 664 Planarity : 0.005 0.058 701 Dihedral : 3.732 14.400 589 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 9.68 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.37), residues: 525 helix: 1.84 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.003 0.001 HIS A 533 PHE 0.013 0.001 PHE A 623 TYR 0.010 0.001 TYR A 606 ARG 0.002 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.465 Fit side-chains REVERT: A 229 MET cc_start: 0.8506 (mmt) cc_final: 0.8211 (mmt) REVERT: A 268 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 465 GLU cc_start: 0.8018 (mt-10) cc_final: 0.6914 (mp0) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.1264 time to fit residues: 15.6389 Evaluate side-chains 88 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140711 restraints weight = 5197.173| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.74 r_work: 0.3655 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4161 Z= 0.214 Angle : 0.586 7.298 5663 Z= 0.289 Chirality : 0.041 0.212 664 Planarity : 0.005 0.054 701 Dihedral : 3.642 16.566 589 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 14.06 % Favored : 84.33 % 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: 1.52 (0.38), residues: 525 helix: 2.00 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.08 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 258 HIS 0.001 0.001 HIS A 96 PHE 0.023 0.001 PHE A 311 TYR 0.011 0.001 TYR A 207 ARG 0.001 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.447 Fit side-chains REVERT: A 254 ILE cc_start: 0.8807 (mm) cc_final: 0.8581 (mt) REVERT: A 465 GLU cc_start: 0.7935 (mt-10) cc_final: 0.6745 (mp0) REVERT: A 611 MET cc_start: 0.8521 (mmm) cc_final: 0.8317 (mmm) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1394 time to fit residues: 16.9429 Evaluate side-chains 83 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** 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 = 0.4165 r_free = 0.4165 target = 0.177258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138839 restraints weight = 5256.808| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.75 r_work: 0.3614 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4161 Z= 0.231 Angle : 0.603 8.069 5663 Z= 0.294 Chirality : 0.042 0.222 664 Planarity : 0.005 0.052 701 Dihedral : 3.621 14.766 589 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.53 % Allowed : 17.05 % Favored : 80.41 % 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: 1.56 (0.38), residues: 525 helix: 2.03 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.012 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.473 Fit side-chains REVERT: A 60 GLU cc_start: 0.7849 (tt0) cc_final: 0.7220 (pt0) REVERT: A 254 ILE cc_start: 0.8812 (mm) cc_final: 0.8560 (mt) REVERT: A 268 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 465 GLU cc_start: 0.7909 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 611 MET cc_start: 0.8456 (mmm) cc_final: 0.8199 (mmm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1211 time to fit residues: 14.4988 Evaluate side-chains 89 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.178928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140474 restraints weight = 5309.071| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.78 r_work: 0.3639 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4161 Z= 0.201 Angle : 0.572 8.495 5663 Z= 0.282 Chirality : 0.041 0.243 664 Planarity : 0.005 0.051 701 Dihedral : 3.571 14.085 589 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.76 % Allowed : 18.43 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.38), residues: 525 helix: 2.13 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.05 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 258 HIS 0.001 0.000 HIS A 119 PHE 0.013 0.001 PHE A 113 TYR 0.009 0.001 TYR A 207 ARG 0.001 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.439 Fit side-chains REVERT: A 60 GLU cc_start: 0.7875 (tt0) cc_final: 0.7301 (pt0) REVERT: A 254 ILE cc_start: 0.8784 (mm) cc_final: 0.8543 (mt) REVERT: A 268 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 310 ASP cc_start: 0.8546 (m-30) cc_final: 0.8240 (m-30) REVERT: A 465 GLU cc_start: 0.7896 (mt-10) cc_final: 0.6766 (mp0) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.1311 time to fit residues: 16.1675 Evaluate side-chains 94 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138777 restraints weight = 5183.850| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.73 r_work: 0.3624 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4161 Z= 0.242 Angle : 0.602 8.750 5663 Z= 0.297 Chirality : 0.042 0.256 664 Planarity : 0.005 0.049 701 Dihedral : 3.599 14.615 589 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.23 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.38), residues: 525 helix: 2.13 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.08 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 PHE 0.013 0.001 PHE A 113 TYR 0.022 0.001 TYR A 207 ARG 0.001 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.449 Fit side-chains REVERT: A 60 GLU cc_start: 0.7871 (tt0) cc_final: 0.7306 (pt0) REVERT: A 254 ILE cc_start: 0.8800 (mm) cc_final: 0.8551 (mt) REVERT: A 268 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 310 ASP cc_start: 0.8570 (m-30) cc_final: 0.8283 (m-30) REVERT: A 465 GLU cc_start: 0.7899 (mt-10) cc_final: 0.6756 (mp0) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.1140 time to fit residues: 14.0428 Evaluate side-chains 89 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.177962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139294 restraints weight = 5233.970| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.75 r_work: 0.3631 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4161 Z= 0.220 Angle : 0.598 9.316 5663 Z= 0.292 Chirality : 0.041 0.254 664 Planarity : 0.005 0.049 701 Dihedral : 3.592 14.303 589 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 19.35 % Favored : 77.88 % 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: 1.63 (0.38), residues: 525 helix: 2.14 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.17 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 PHE 0.014 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.002 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.418 Fit side-chains REVERT: A 268 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 310 ASP cc_start: 0.8567 (m-30) cc_final: 0.8288 (m-30) REVERT: A 465 GLU cc_start: 0.7863 (mt-10) cc_final: 0.6743 (mp0) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.1146 time to fit residues: 13.5032 Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 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 177 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139951 restraints weight = 5171.426| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.73 r_work: 0.3639 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4161 Z= 0.215 Angle : 0.587 9.703 5663 Z= 0.289 Chirality : 0.042 0.279 664 Planarity : 0.005 0.049 701 Dihedral : 3.585 14.096 589 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.00 % Allowed : 19.35 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 525 helix: 2.11 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.016 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.410 Fit side-chains REVERT: A 268 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7795 (mm) REVERT: A 310 ASP cc_start: 0.8552 (m-30) cc_final: 0.8282 (m-30) REVERT: A 415 LEU cc_start: 0.8533 (tp) cc_final: 0.8320 (tp) REVERT: A 465 GLU cc_start: 0.7863 (mt-10) cc_final: 0.6756 (mp0) REVERT: A 611 MET cc_start: 0.8548 (mmm) cc_final: 0.8341 (mmm) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.1135 time to fit residues: 14.2109 Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138504 restraints weight = 5235.733| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.75 r_work: 0.3616 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4161 Z= 0.260 Angle : 0.622 9.748 5663 Z= 0.309 Chirality : 0.042 0.276 664 Planarity : 0.005 0.048 701 Dihedral : 3.659 14.540 589 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.30 % Allowed : 20.97 % Favored : 76.73 % 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: 1.54 (0.37), residues: 525 helix: 2.05 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.010 0.001 PHE A 212 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.479 Fit side-chains REVERT: A 268 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 310 ASP cc_start: 0.8590 (m-30) cc_final: 0.8329 (m-30) REVERT: A 415 LEU cc_start: 0.8529 (tp) cc_final: 0.8292 (tp) REVERT: A 465 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6786 (mp0) REVERT: A 611 MET cc_start: 0.8533 (mmm) cc_final: 0.8261 (mmm) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.1483 time to fit residues: 17.6704 Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140958 restraints weight = 5228.899| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.77 r_work: 0.3646 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4161 Z= 0.217 Angle : 0.609 9.883 5663 Z= 0.302 Chirality : 0.042 0.287 664 Planarity : 0.005 0.048 701 Dihedral : 3.667 13.874 589 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.53 % Allowed : 21.20 % Favored : 76.27 % 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: 1.64 (0.38), residues: 525 helix: 2.12 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.09 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 258 HIS 0.002 0.001 HIS A 119 PHE 0.017 0.001 PHE A 113 TYR 0.021 0.001 TYR A 207 ARG 0.001 0.000 ARG A 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.458 Fit side-chains REVERT: A 268 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7794 (mm) REVERT: A 310 ASP cc_start: 0.8588 (m-30) cc_final: 0.8317 (m-30) REVERT: A 415 LEU cc_start: 0.8475 (tp) cc_final: 0.8209 (tp) REVERT: A 465 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6735 (mp0) REVERT: A 611 MET cc_start: 0.8614 (mmm) cc_final: 0.8188 (mmm) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.1174 time to fit residues: 14.8263 Evaluate side-chains 92 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** 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 = 0.4191 r_free = 0.4191 target = 0.179555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141250 restraints weight = 5220.303| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.74 r_work: 0.3646 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4161 Z= 0.230 Angle : 0.641 9.729 5663 Z= 0.315 Chirality : 0.042 0.284 664 Planarity : 0.005 0.048 701 Dihedral : 3.892 33.958 589 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.84 % Allowed : 22.12 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.61 (0.38), residues: 525 helix: 2.11 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 258 HIS 0.002 0.000 HIS A 119 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 606 ARG 0.002 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.57 seconds wall clock time: 36 minutes 41.43 seconds (2201.43 seconds total)