Starting phenix.real_space_refine on Thu Nov 14 04:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_37233.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_37233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_37233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_37233.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgv_37233/11_2024/8kgv_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-5513/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: 3.13, per 1000 atoms: 0.77 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: 1.11 Conformation dependent library (CDL) restraints added in 672.0 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: 0.44 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: 1.24 Time building geometry restraints manager: 1.27 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: 0.600 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- 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 : 0.465 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: 0.1486 time to fit residues: 19.7816 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 : 0.429 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.003 0.038 4161 Z= 0.231 Angle : 0.628 7.480 5663 Z= 0.309 Chirality : 0.042 0.197 664 Planarity : 0.005 0.059 701 Dihedral : 3.735 14.386 589 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.70 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: 1.29 (0.37), residues: 525 helix: 1.82 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 : 0.508 Fit side-chains REVERT: A 229 MET cc_start: 0.8490 (mmt) cc_final: 0.8179 (mmt) REVERT: A 268 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 465 GLU cc_start: 0.7840 (mt-10) cc_final: 0.6818 (mp0) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.1538 time to fit residues: 18.5384 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 : 0.426 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4161 Z= 0.240 Angle : 0.595 7.333 5663 Z= 0.293 Chirality : 0.042 0.211 664 Planarity : 0.005 0.054 701 Dihedral : 3.662 17.218 589 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 14.06 % Favored : 84.10 % 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: 1.47 (0.38), residues: 525 helix: 1.96 (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 0.009 0.001 TRP A 258 HIS 0.001 0.001 HIS A 96 PHE 0.022 0.001 PHE A 311 TYR 0.010 0.001 TYR A 606 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 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.420 Fit side-chains REVERT: A 229 MET cc_start: 0.8530 (mmt) cc_final: 0.8321 (mmt) REVERT: A 254 ILE cc_start: 0.8763 (mm) cc_final: 0.8538 (mt) REVERT: A 465 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6777 (mp0) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1334 time to fit residues: 15.7871 Evaluate side-chains 84 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4161 Z= 0.215 Angle : 0.586 7.983 5663 Z= 0.289 Chirality : 0.041 0.231 664 Planarity : 0.005 0.052 701 Dihedral : 3.622 14.738 589 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 16.82 % Favored : 81.34 % 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: 1.57 (0.38), residues: 525 helix: 2.06 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.09 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 321 *********************** 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 95 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.468 Fit side-chains REVERT: A 254 ILE cc_start: 0.8745 (mm) cc_final: 0.8529 (mt) REVERT: A 268 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 465 GLU cc_start: 0.7753 (mt-10) cc_final: 0.6751 (mp0) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1269 time to fit residues: 14.9940 Evaluate side-chains 87 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 268 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 29 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 40.0000 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4161 Z= 0.215 Angle : 0.586 8.523 5663 Z= 0.287 Chirality : 0.041 0.216 664 Planarity : 0.005 0.050 701 Dihedral : 3.583 14.685 589 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.00 % Allowed : 17.74 % Favored : 79.26 % 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: 2.11 (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 0.014 0.001 TRP A 258 HIS 0.001 0.000 HIS A 96 PHE 0.013 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 *********************** 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: 13 poor density : 88 time to evaluate : 0.473 Fit side-chains REVERT: A 60 GLU cc_start: 0.7663 (tt0) cc_final: 0.7073 (pt0) REVERT: A 254 ILE cc_start: 0.8737 (mm) cc_final: 0.8517 (mt) REVERT: A 268 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7750 (mm) REVERT: A 310 ASP cc_start: 0.8154 (m-30) cc_final: 0.7855 (m-30) REVERT: A 465 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6728 (mp0) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1272 time to fit residues: 15.7179 Evaluate side-chains 90 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4161 Z= 0.201 Angle : 0.591 8.730 5663 Z= 0.287 Chirality : 0.041 0.216 664 Planarity : 0.005 0.050 701 Dihedral : 3.558 14.049 589 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.00 % Allowed : 19.82 % Favored : 77.19 % 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: 1.72 (0.38), residues: 525 helix: 2.19 (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 0.008 0.001 TYR A 606 ARG 0.002 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: 13 poor density : 85 time to evaluate : 0.428 Fit side-chains REVERT: A 268 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7749 (mm) REVERT: A 310 ASP cc_start: 0.8166 (m-30) cc_final: 0.7886 (m-30) REVERT: A 465 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6711 (mp0) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1279 time to fit residues: 15.3821 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 : 0.403 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2179 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= 0.225 Angle : 0.592 9.334 5663 Z= 0.289 Chirality : 0.041 0.212 664 Planarity : 0.005 0.049 701 Dihedral : 3.549 14.317 589 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.53 % Allowed : 19.35 % Favored : 78.11 % 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: 2.14 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.12 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.014 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 252 *********************** 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 99 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.479 Fit side-chains REVERT: A 268 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7752 (mm) REVERT: A 310 ASP cc_start: 0.8198 (m-30) cc_final: 0.7935 (m-30) REVERT: A 465 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6733 (mp0) REVERT: A 611 MET cc_start: 0.8422 (mmm) cc_final: 0.8174 (mmm) outliers start: 11 outliers final: 10 residues processed: 92 average time/residue: 0.1368 time to fit residues: 16.6931 Evaluate side-chains 96 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4161 Z= 0.239 Angle : 0.612 9.278 5663 Z= 0.297 Chirality : 0.042 0.211 664 Planarity : 0.005 0.049 701 Dihedral : 3.555 14.520 589 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.00 % Allowed : 20.51 % Favored : 76.50 % 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: 1.61 (0.37), residues: 525 helix: 2.11 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.12 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 PHE 0.017 0.001 PHE A 113 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 252 *********************** 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 99 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.482 Fit side-chains REVERT: A 268 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 310 ASP cc_start: 0.8206 (m-30) cc_final: 0.7947 (m-30) REVERT: A 465 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6764 (mp0) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.1342 time to fit residues: 16.2976 Evaluate side-chains 92 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4161 Z= 0.182 Angle : 0.606 9.549 5663 Z= 0.290 Chirality : 0.041 0.212 664 Planarity : 0.004 0.049 701 Dihedral : 3.540 13.377 589 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.00 % Allowed : 20.74 % 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: 1.74 (0.38), residues: 525 helix: 2.21 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.10 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.017 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 *********************** 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 99 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.459 Fit side-chains REVERT: A 268 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 310 ASP cc_start: 0.8186 (m-30) cc_final: 0.7944 (m-30) REVERT: A 311 PHE cc_start: 0.7395 (t80) cc_final: 0.7104 (t80) REVERT: A 465 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6679 (mp0) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1180 time to fit residues: 14.7127 Evaluate side-chains 96 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 38 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4161 Z= 0.219 Angle : 0.630 9.544 5663 Z= 0.303 Chirality : 0.042 0.210 664 Planarity : 0.005 0.048 701 Dihedral : 3.565 13.402 589 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 21.66 % Favored : 76.04 % 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 : -1.11 (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 212 TYR 0.013 0.001 TYR A 90 ARG 0.001 0.000 ARG A 280 ********************** 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 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.473 Fit side-chains REVERT: A 268 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 310 ASP cc_start: 0.8190 (m-30) cc_final: 0.7950 (m-30) REVERT: A 465 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6716 (mp0) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.1190 time to fit residues: 14.5644 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 : 0.441 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 28 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 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140139 restraints weight = 5293.881| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.79 r_work: 0.3620 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4161 Z= 0.213 Angle : 0.620 9.722 5663 Z= 0.298 Chirality : 0.042 0.212 664 Planarity : 0.005 0.048 701 Dihedral : 3.539 12.873 589 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.53 % Allowed : 21.43 % Favored : 76.04 % 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: 1.68 (0.38), residues: 525 helix: 2.17 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.11 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 258 HIS 0.002 0.001 HIS A 119 PHE 0.018 0.001 PHE A 113 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.47 seconds wall clock time: 23 minutes 47.24 seconds (1427.24 seconds total)