Starting phenix.real_space_refine on Fri Aug 22 14:22:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgv_37233/08_2025/8kgv_37233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgv_37233/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kgv_37233/08_2025/8kgv_37233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgv_37233/08_2025/8kgv_37233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgv_37233/08_2025/8kgv_37233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgv_37233/08_2025/8kgv_37233.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.38 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: 0.43 Conformation dependent library (CDL) restraints added in 230.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 0.61 Time building geometry restraints manager: 0.60 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- 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 4168 Z= 0.282 Angle : 0.809 10.766 5678 Z= 0.450 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 605 TYR 0.016 0.001 TYR A 429 PHE 0.025 0.001 PHE A 217 TRP 0.026 0.002 TRP A 258 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 4161) covalent geometry : angle 0.80235 ( 5663) SS BOND : bond 0.00386 ( 6) SS BOND : angle 0.91358 ( 12) hydrogen bonds : bond 0.15965 ( 259) hydrogen bonds : angle 6.13845 ( 765) link_NAG-ASN : bond 0.01031 ( 1) link_NAG-ASN : angle 4.34004 ( 3) *********************** 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 : 0.155 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: 0.0724 time to fit residues: 9.5916 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.178293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139697 restraints weight = 5269.355| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.76 r_work: 0.3634 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4168 Z= 0.161 Angle : 0.638 7.463 5678 Z= 0.314 Chirality : 0.042 0.203 664 Planarity : 0.005 0.057 701 Dihedral : 3.741 14.879 589 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 9.68 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.37), residues: 525 helix: 1.80 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 94 TYR 0.011 0.001 TYR A 606 PHE 0.012 0.001 PHE A 623 TRP 0.016 0.001 TRP A 258 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4161) covalent geometry : angle 0.63630 ( 5663) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.93280 ( 12) hydrogen bonds : bond 0.04256 ( 259) hydrogen bonds : angle 4.33659 ( 765) link_NAG-ASN : bond 0.00329 ( 1) link_NAG-ASN : angle 1.66398 ( 3) *********************** 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: 8 poor density : 89 time to evaluate : 0.165 Fit side-chains REVERT: A 229 MET cc_start: 0.8396 (mmt) cc_final: 0.8093 (mmt) REVERT: A 268 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7774 (mm) REVERT: A 465 GLU cc_start: 0.8015 (mt-10) cc_final: 0.6863 (mp0) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 0.0539 time to fit residues: 6.7725 Evaluate side-chains 84 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.177045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138461 restraints weight = 5166.011| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.72 r_work: 0.3630 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4168 Z= 0.142 Angle : 0.594 7.430 5678 Z= 0.293 Chirality : 0.042 0.205 664 Planarity : 0.005 0.053 701 Dihedral : 3.673 17.488 589 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.30 % Allowed : 13.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.38), residues: 525 helix: 1.97 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.09 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.010 0.001 TYR A 606 PHE 0.022 0.001 PHE A 311 TRP 0.009 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4161) covalent geometry : angle 0.59259 ( 5663) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.87397 ( 12) hydrogen bonds : bond 0.03722 ( 259) hydrogen bonds : angle 4.14518 ( 765) link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 1.47050 ( 3) *********************** 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 101 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.145 Fit side-chains REVERT: A 60 GLU cc_start: 0.7848 (tt0) cc_final: 0.7250 (pt0) REVERT: A 229 MET cc_start: 0.8434 (mmt) cc_final: 0.8233 (mmt) REVERT: A 254 ILE cc_start: 0.8836 (mm) cc_final: 0.8572 (mt) REVERT: A 268 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 465 GLU cc_start: 0.7952 (mt-10) cc_final: 0.6864 (mp0) REVERT: A 611 MET cc_start: 0.8538 (mmm) cc_final: 0.8320 (mmm) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0561 time to fit residues: 6.9740 Evaluate side-chains 85 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.178629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140432 restraints weight = 5146.237| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.70 r_work: 0.3634 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4168 Z= 0.128 Angle : 0.589 7.963 5678 Z= 0.290 Chirality : 0.041 0.210 664 Planarity : 0.005 0.052 701 Dihedral : 3.627 14.787 589 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.07 % Allowed : 16.36 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.38), residues: 525 helix: 2.07 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.09 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.008 0.001 TYR A 606 PHE 0.011 0.001 PHE A 113 TRP 0.010 0.001 TRP A 258 HIS 0.001 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4161) covalent geometry : angle 0.58665 ( 5663) SS BOND : bond 0.00235 ( 6) SS BOND : angle 1.02640 ( 12) hydrogen bonds : bond 0.03511 ( 259) hydrogen bonds : angle 4.03363 ( 765) link_NAG-ASN : bond 0.00347 ( 1) link_NAG-ASN : angle 1.38006 ( 3) *********************** 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 100 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.157 Fit side-chains REVERT: A 60 GLU cc_start: 0.7863 (tt0) cc_final: 0.7262 (pt0) REVERT: A 254 ILE cc_start: 0.8819 (mm) cc_final: 0.8558 (mt) REVERT: A 465 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6729 (mp0) REVERT: A 611 MET cc_start: 0.8449 (mmm) cc_final: 0.8199 (mmm) outliers start: 9 outliers final: 9 residues processed: 93 average time/residue: 0.0565 time to fit residues: 7.0244 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 : 0.169 ------------------------------------------------------------------------------- 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 367 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 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4168 r_free = 0.4168 target = 0.177462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139200 restraints weight = 5190.449| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.71 r_work: 0.3633 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4168 Z= 0.135 Angle : 0.600 8.553 5678 Z= 0.290 Chirality : 0.041 0.210 664 Planarity : 0.005 0.051 701 Dihedral : 3.589 14.853 589 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.23 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.38), residues: 525 helix: 2.08 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.10 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.009 0.001 TYR A 606 PHE 0.013 0.001 PHE A 113 TRP 0.013 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4161) covalent geometry : angle 0.59821 ( 5663) SS BOND : bond 0.00226 ( 6) SS BOND : angle 1.04316 ( 12) hydrogen bonds : bond 0.03426 ( 259) hydrogen bonds : angle 4.03506 ( 765) link_NAG-ASN : bond 0.00337 ( 1) link_NAG-ASN : angle 1.31418 ( 3) *********************** 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 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.180 Fit side-chains REVERT: A 60 GLU cc_start: 0.7861 (tt0) cc_final: 0.7294 (pt0) REVERT: A 254 ILE cc_start: 0.8797 (mm) cc_final: 0.8530 (mt) REVERT: A 268 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 310 ASP cc_start: 0.8544 (m-30) cc_final: 0.8234 (m-30) REVERT: A 465 GLU cc_start: 0.7880 (mt-10) cc_final: 0.6715 (mp0) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.0463 time to fit residues: 5.5452 Evaluate side-chains 92 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 367 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 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.175622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136728 restraints weight = 5328.803| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.77 r_work: 0.3605 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4168 Z= 0.146 Angle : 0.595 8.848 5678 Z= 0.291 Chirality : 0.041 0.208 664 Planarity : 0.005 0.050 701 Dihedral : 3.610 15.222 589 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.46 % Allowed : 19.59 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.38), residues: 525 helix: 2.06 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.13 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 605 TYR 0.010 0.001 TYR A 606 PHE 0.013 0.001 PHE A 113 TRP 0.015 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4161) covalent geometry : angle 0.59226 ( 5663) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.28143 ( 12) hydrogen bonds : bond 0.03509 ( 259) hydrogen bonds : angle 4.05242 ( 765) link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 1.24936 ( 3) *********************** 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 100 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.154 Fit side-chains REVERT: A 60 GLU cc_start: 0.7875 (tt0) cc_final: 0.7371 (pt0) REVERT: A 254 ILE cc_start: 0.8797 (mm) cc_final: 0.8531 (mt) REVERT: A 268 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 310 ASP cc_start: 0.8558 (m-30) cc_final: 0.8264 (m-30) REVERT: A 465 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6779 (mp0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.0498 time to fit residues: 6.3182 Evaluate side-chains 92 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 367 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 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137433 restraints weight = 5340.019| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.75 r_work: 0.3612 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4168 Z= 0.144 Angle : 0.610 9.386 5678 Z= 0.296 Chirality : 0.041 0.207 664 Planarity : 0.005 0.049 701 Dihedral : 3.625 15.267 589 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.00 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.38), residues: 525 helix: 2.08 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.17 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.010 0.001 TYR A 606 PHE 0.014 0.001 PHE A 113 TRP 0.017 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4161) covalent geometry : angle 0.60676 ( 5663) SS BOND : bond 0.00229 ( 6) SS BOND : angle 1.44425 ( 12) hydrogen bonds : bond 0.03502 ( 259) hydrogen bonds : angle 4.07253 ( 765) link_NAG-ASN : bond 0.00341 ( 1) link_NAG-ASN : angle 1.22592 ( 3) *********************** 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 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.166 Fit side-chains REVERT: A 60 GLU cc_start: 0.7888 (tt0) cc_final: 0.7373 (pt0) REVERT: A 268 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 310 ASP cc_start: 0.8540 (m-30) cc_final: 0.8256 (m-30) REVERT: A 465 GLU cc_start: 0.7908 (mt-10) cc_final: 0.6786 (mp0) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.0557 time to fit residues: 6.7286 Evaluate side-chains 93 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 367 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 7 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4162 r_free = 0.4162 target = 0.176691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138396 restraints weight = 5232.120| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.71 r_work: 0.3626 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4168 Z= 0.133 Angle : 0.604 9.505 5678 Z= 0.293 Chirality : 0.041 0.203 664 Planarity : 0.005 0.049 701 Dihedral : 3.630 14.960 589 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.00 % Allowed : 20.05 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.38), residues: 525 helix: 2.11 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.009 0.001 TYR A 606 PHE 0.016 0.001 PHE A 113 TRP 0.021 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4161) covalent geometry : angle 0.59930 ( 5663) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.58988 ( 12) hydrogen bonds : bond 0.03444 ( 259) hydrogen bonds : angle 4.05293 ( 765) link_NAG-ASN : bond 0.00349 ( 1) link_NAG-ASN : angle 1.20313 ( 3) *********************** 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 96 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: A 60 GLU cc_start: 0.7889 (tt0) cc_final: 0.7351 (pt0) REVERT: A 268 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 310 ASP cc_start: 0.8548 (m-30) cc_final: 0.8271 (m-30) REVERT: A 465 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6767 (mp0) REVERT: A 611 MET cc_start: 0.8595 (mmm) cc_final: 0.8390 (mmm) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.0542 time to fit residues: 6.4603 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 : 0.159 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 42 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.178451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139794 restraints weight = 5319.476| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.78 r_work: 0.3638 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4168 Z= 0.125 Angle : 0.613 10.202 5678 Z= 0.294 Chirality : 0.042 0.202 664 Planarity : 0.005 0.049 701 Dihedral : 3.612 14.092 589 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.38), residues: 525 helix: 2.12 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 605 TYR 0.008 0.001 TYR A 606 PHE 0.008 0.001 PHE A 212 TRP 0.022 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4161) covalent geometry : angle 0.60980 ( 5663) SS BOND : bond 0.00201 ( 6) SS BOND : angle 1.31423 ( 12) hydrogen bonds : bond 0.03387 ( 259) hydrogen bonds : angle 4.04149 ( 765) link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 1.20622 ( 3) *********************** 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 : 0.090 Fit side-chains REVERT: A 60 GLU cc_start: 0.7887 (tt0) cc_final: 0.7342 (pt0) REVERT: A 268 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 310 ASP cc_start: 0.8563 (m-30) cc_final: 0.8300 (m-30) REVERT: A 465 GLU cc_start: 0.7846 (mt-10) cc_final: 0.6769 (mp0) REVERT: A 538 MET cc_start: 0.8359 (mmp) cc_final: 0.8145 (mmp) REVERT: A 611 MET cc_start: 0.8570 (mmm) cc_final: 0.8306 (mmm) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.0456 time to fit residues: 5.6856 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 : 0.149 ------------------------------------------------------------------------------- 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 22 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139838 restraints weight = 5287.128| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.84 r_work: 0.3647 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4168 Z= 0.119 Angle : 0.609 9.806 5678 Z= 0.291 Chirality : 0.042 0.202 664 Planarity : 0.005 0.049 701 Dihedral : 3.582 15.236 589 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.38), residues: 525 helix: 2.13 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 605 TYR 0.008 0.001 TYR A 357 PHE 0.022 0.001 PHE A 113 TRP 0.024 0.002 TRP A 258 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4161) covalent geometry : angle 0.60668 ( 5663) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.20433 ( 12) hydrogen bonds : bond 0.03360 ( 259) hydrogen bonds : angle 4.01811 ( 765) link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 1.18710 ( 3) ********************** 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 : 0.167 Fit side-chains REVERT: A 60 GLU cc_start: 0.7881 (tt0) cc_final: 0.7346 (pt0) REVERT: A 268 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (mm) REVERT: A 310 ASP cc_start: 0.8576 (m-30) cc_final: 0.8310 (m-30) REVERT: A 465 GLU cc_start: 0.7793 (mt-10) cc_final: 0.6682 (mp0) REVERT: A 611 MET cc_start: 0.8582 (mmm) cc_final: 0.8165 (mmm) outliers start: 10 outliers final: 9 residues processed: 92 average time/residue: 0.0476 time to fit residues: 6.0337 Evaluate side-chains 93 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.180073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141698 restraints weight = 5215.168| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.77 r_work: 0.3652 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4168 Z= 0.129 Angle : 0.638 10.310 5678 Z= 0.303 Chirality : 0.042 0.201 664 Planarity : 0.005 0.049 701 Dihedral : 3.598 14.099 589 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 21.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.38), residues: 525 helix: 2.11 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.010 0.001 TYR A 90 PHE 0.017 0.001 PHE A 113 TRP 0.024 0.002 TRP A 258 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4161) covalent geometry : angle 0.63595 ( 5663) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.18477 ( 12) hydrogen bonds : bond 0.03424 ( 259) hydrogen bonds : angle 4.00832 ( 765) link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 1.14771 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 989.72 seconds wall clock time: 17 minutes 37.21 seconds (1057.21 seconds total)