Starting phenix.real_space_refine on Sun Apr 27 01:15:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgv_37233/04_2025/8kgv_37233.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2673 2.51 5 N 652 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 2.96, per 1000 atoms: 0.73 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: 0.93 Conformation dependent library (CDL) restraints added in 467.7 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: 0.38 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: 1.12 Time building geometry restraints manager: 1.12 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.01031 ( 1) link_NAG-ASN : angle 4.34004 ( 3) hydrogen bonds : bond 0.15965 ( 259) hydrogen bonds : angle 6.13845 ( 765) SS BOND : bond 0.00386 ( 6) SS BOND : angle 0.91358 ( 12) covalent geometry : bond 0.00459 ( 4161) covalent geometry : angle 0.80235 ( 5663) *********************** 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 : 0.427 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: 0.1459 time to fit residues: 19.3547 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 : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.179339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140765 restraints weight = 5210.642| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.77 r_work: 0.3651 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4168 Z= 0.145 Angle : 0.628 7.475 5678 Z= 0.308 Chirality : 0.042 0.195 664 Planarity : 0.005 0.058 701 Dihedral : 3.732 14.400 589 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 9.68 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.37), residues: 525 helix: 1.84 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.003 0.001 HIS A 533 PHE 0.013 0.001 PHE A 623 TYR 0.010 0.001 TYR A 606 ARG 0.002 0.000 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 1) link_NAG-ASN : angle 1.63811 ( 3) hydrogen bonds : bond 0.04165 ( 259) hydrogen bonds : angle 4.29708 ( 765) SS BOND : bond 0.00458 ( 6) SS BOND : angle 0.87243 ( 12) covalent geometry : bond 0.00350 ( 4161) covalent geometry : angle 0.62669 ( 5663) *********************** 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 : 0.396 Fit side-chains REVERT: A 229 MET cc_start: 0.8506 (mmt) cc_final: 0.8211 (mmt) REVERT: A 268 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 465 GLU cc_start: 0.8018 (mt-10) cc_final: 0.6914 (mp0) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.1208 time to fit residues: 14.7997 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 : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140711 restraints weight = 5197.173| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.74 r_work: 0.3655 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4168 Z= 0.132 Angle : 0.588 7.298 5678 Z= 0.289 Chirality : 0.041 0.212 664 Planarity : 0.005 0.054 701 Dihedral : 3.642 16.566 589 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 14.06 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.38), residues: 525 helix: 2.00 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.08 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 258 HIS 0.001 0.001 HIS A 96 PHE 0.023 0.001 PHE A 311 TYR 0.011 0.001 TYR A 207 ARG 0.001 0.000 ARG A 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 1.51798 ( 3) hydrogen bonds : bond 0.03670 ( 259) hydrogen bonds : angle 4.11659 ( 765) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.89014 ( 12) covalent geometry : bond 0.00323 ( 4161) covalent geometry : angle 0.58608 ( 5663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.458 Fit side-chains REVERT: A 254 ILE cc_start: 0.8807 (mm) cc_final: 0.8581 (mt) REVERT: A 465 GLU cc_start: 0.7935 (mt-10) cc_final: 0.6745 (mp0) REVERT: A 611 MET cc_start: 0.8521 (mmm) cc_final: 0.8317 (mmm) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1252 time to fit residues: 15.3298 Evaluate side-chains 83 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138839 restraints weight = 5256.808| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.75 r_work: 0.3614 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4168 Z= 0.142 Angle : 0.605 8.069 5678 Z= 0.295 Chirality : 0.042 0.222 664 Planarity : 0.005 0.052 701 Dihedral : 3.621 14.766 589 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.53 % Allowed : 17.05 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.38), residues: 525 helix: 2.03 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.002 0.001 HIS A 96 PHE 0.012 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 1) link_NAG-ASN : angle 1.38193 ( 3) hydrogen bonds : bond 0.03584 ( 259) hydrogen bonds : angle 4.06632 ( 765) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.13593 ( 12) covalent geometry : bond 0.00347 ( 4161) covalent geometry : angle 0.60255 ( 5663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.422 Fit side-chains REVERT: A 60 GLU cc_start: 0.7849 (tt0) cc_final: 0.7220 (pt0) REVERT: A 254 ILE cc_start: 0.8812 (mm) cc_final: 0.8560 (mt) REVERT: A 268 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 465 GLU cc_start: 0.7909 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 611 MET cc_start: 0.8456 (mmm) cc_final: 0.8199 (mmm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1215 time to fit residues: 14.6158 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 : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139828 restraints weight = 5318.898| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.78 r_work: 0.3643 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1958 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= 0.128 Angle : 0.577 8.520 5678 Z= 0.284 Chirality : 0.041 0.241 664 Planarity : 0.005 0.051 701 Dihedral : 3.574 14.180 589 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.76 % Allowed : 18.66 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.38), residues: 525 helix: 2.12 (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 119 PHE 0.013 0.001 PHE A 113 TYR 0.009 0.001 TYR A 207 ARG 0.001 0.000 ARG A 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 1) link_NAG-ASN : angle 1.34709 ( 3) hydrogen bonds : bond 0.03425 ( 259) hydrogen bonds : angle 4.00779 ( 765) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.05240 ( 12) covalent geometry : bond 0.00306 ( 4161) covalent geometry : angle 0.57517 ( 5663) *********************** 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 100 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.448 Fit side-chains REVERT: A 60 GLU cc_start: 0.7867 (tt0) cc_final: 0.7294 (pt0) REVERT: A 254 ILE cc_start: 0.8789 (mm) cc_final: 0.8540 (mt) REVERT: A 268 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7853 (mm) REVERT: A 310 ASP cc_start: 0.8543 (m-30) cc_final: 0.8232 (m-30) REVERT: A 465 GLU cc_start: 0.7894 (mt-10) cc_final: 0.6744 (mp0) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.1187 time to fit residues: 14.5427 Evaluate side-chains 93 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.178604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139898 restraints weight = 5187.191| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.75 r_work: 0.3637 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2090 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 8.751 5678 Z= 0.287 Chirality : 0.041 0.258 664 Planarity : 0.005 0.050 701 Dihedral : 3.571 14.159 589 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.76 % Allowed : 19.59 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.38), residues: 525 helix: 2.16 (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 0.016 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 PHE 0.014 0.001 PHE A 113 TYR 0.008 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 1.28578 ( 3) hydrogen bonds : bond 0.03428 ( 259) hydrogen bonds : angle 4.00056 ( 765) SS BOND : bond 0.00197 ( 6) SS BOND : angle 1.25203 ( 12) covalent geometry : bond 0.00310 ( 4161) covalent geometry : angle 0.58659 ( 5663) *********************** 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 96 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.414 Fit side-chains REVERT: A 254 ILE cc_start: 0.8785 (mm) cc_final: 0.8546 (mt) REVERT: A 268 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 310 ASP cc_start: 0.8590 (m-30) cc_final: 0.8307 (m-30) REVERT: A 465 GLU cc_start: 0.7860 (mt-10) cc_final: 0.6731 (mp0) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1156 time to fit residues: 14.1857 Evaluate side-chains 87 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.178473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139809 restraints weight = 5206.340| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.73 r_work: 0.3636 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4168 Z= 0.123 Angle : 0.598 9.344 5678 Z= 0.287 Chirality : 0.041 0.234 664 Planarity : 0.004 0.049 701 Dihedral : 3.538 13.625 589 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.00 % Allowed : 19.35 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.38), residues: 525 helix: 2.18 (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 0.018 0.001 TRP A 258 HIS 0.002 0.000 HIS A 96 PHE 0.015 0.001 PHE A 113 TYR 0.009 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 1.25005 ( 3) hydrogen bonds : bond 0.03431 ( 259) hydrogen bonds : angle 4.01505 ( 765) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.90821 ( 12) covalent geometry : bond 0.00294 ( 4161) covalent geometry : angle 0.59705 ( 5663) *********************** 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 : 0.420 Fit side-chains REVERT: A 268 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 310 ASP cc_start: 0.8574 (m-30) cc_final: 0.8292 (m-30) REVERT: A 465 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6710 (mp0) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.1137 time to fit residues: 13.9566 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 : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.176491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137377 restraints weight = 5263.131| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.80 r_work: 0.3610 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2276 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= 0.145 Angle : 0.608 9.852 5678 Z= 0.295 Chirality : 0.043 0.272 664 Planarity : 0.004 0.048 701 Dihedral : 3.566 14.202 589 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.53 % Allowed : 19.82 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.37), residues: 525 helix: 2.07 (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 0.019 0.001 PHE A 113 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 1) link_NAG-ASN : angle 1.18764 ( 3) hydrogen bonds : bond 0.03509 ( 259) hydrogen bonds : angle 4.05794 ( 765) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.36597 ( 12) covalent geometry : bond 0.00361 ( 4161) covalent geometry : angle 0.60495 ( 5663) *********************** 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 98 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.412 Fit side-chains REVERT: A 268 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7760 (mm) REVERT: A 310 ASP cc_start: 0.8570 (m-30) cc_final: 0.8300 (m-30) REVERT: A 465 GLU cc_start: 0.7852 (mt-10) cc_final: 0.6759 (mp0) REVERT: A 611 MET cc_start: 0.8572 (mmm) cc_final: 0.8365 (mmm) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.1120 time to fit residues: 13.9900 Evaluate side-chains 87 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.177284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138156 restraints weight = 5286.444| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.81 r_work: 0.3621 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2352 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= 0.138 Angle : 0.624 10.107 5678 Z= 0.301 Chirality : 0.042 0.257 664 Planarity : 0.005 0.048 701 Dihedral : 3.587 13.874 589 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 20.97 % 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: 1.61 (0.38), 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 0.023 0.001 TRP A 258 HIS 0.001 0.000 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 1) link_NAG-ASN : angle 1.17961 ( 3) hydrogen bonds : bond 0.03474 ( 259) hydrogen bonds : angle 4.06991 ( 765) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.74839 ( 12) covalent geometry : bond 0.00339 ( 4161) covalent geometry : angle 0.61853 ( 5663) *********************** 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 97 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.448 Fit side-chains REVERT: A 268 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 310 ASP cc_start: 0.8580 (m-30) cc_final: 0.8318 (m-30) REVERT: A 415 LEU cc_start: 0.8507 (tp) cc_final: 0.8291 (tp) REVERT: A 465 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6751 (mp0) REVERT: A 611 MET cc_start: 0.8571 (mmm) cc_final: 0.8133 (mmm) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1196 time to fit residues: 14.6544 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.176399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137297 restraints weight = 5342.554| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.82 r_work: 0.3603 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4168 Z= 0.148 Angle : 0.641 10.511 5678 Z= 0.307 Chirality : 0.043 0.272 664 Planarity : 0.005 0.048 701 Dihedral : 3.592 14.395 589 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.76 % Allowed : 21.66 % Favored : 75.58 % 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: 1.59 (0.37), 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 TRP 0.024 0.002 TRP A 258 HIS 0.002 0.000 HIS A 119 PHE 0.020 0.001 PHE A 113 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 1.13904 ( 3) hydrogen bonds : bond 0.03517 ( 259) hydrogen bonds : angle 4.11341 ( 765) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.61001 ( 12) covalent geometry : bond 0.00367 ( 4161) covalent geometry : angle 0.63741 ( 5663) ********************** 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 95 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.458 Fit side-chains REVERT: A 268 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 310 ASP cc_start: 0.8599 (m-30) cc_final: 0.8341 (m-30) REVERT: A 465 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6758 (mp0) REVERT: A 611 MET cc_start: 0.8583 (mmm) cc_final: 0.8138 (mmm) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1164 time to fit residues: 13.9422 Evaluate side-chains 94 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 4 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.178974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140545 restraints weight = 5221.339| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.75 r_work: 0.3644 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2469 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= 0.128 Angle : 0.632 10.012 5678 Z= 0.302 Chirality : 0.042 0.267 664 Planarity : 0.005 0.049 701 Dihedral : 3.572 13.774 589 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 22.58 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.38), residues: 525 helix: 2.15 (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 0.024 0.001 TRP A 258 HIS 0.002 0.000 HIS A 119 PHE 0.022 0.001 PHE A 113 TYR 0.010 0.001 TYR A 606 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 1.16327 ( 3) hydrogen bonds : bond 0.03394 ( 259) hydrogen bonds : angle 4.06890 ( 765) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.41210 ( 12) covalent geometry : bond 0.00309 ( 4161) covalent geometry : angle 0.62882 ( 5663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.51 seconds wall clock time: 36 minutes 26.18 seconds (2186.18 seconds total)