Starting phenix.real_space_refine on Wed Jun 3 12:02:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.map" model { file = "/net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opq_70721/06_2026/9opq_70721.cif" } resolution = 3.3 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= 0.001 sd= 0.049 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 44 5.16 5 C 2933 2.51 5 N 818 2.21 5 O 777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2067 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 10, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2421 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 325} Chain breaks: 4 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASN:plan1': 10, 'ASP:plan': 11, 'GLU:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.36, per 1000 atoms: 0.30 Number of scatterers: 4572 At special positions: 0 Unit cell: (64.662, 76.268, 126.837, 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 44 16.00 O 777 8.00 N 818 7.00 C 2933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " 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 470 " " NAG A 702 " - " ASN A 433 " " NAG A 703 " - " ASN A 355 " " NAG A 704 " - " ASN A 454 " " NAG B2001 " - " ASN B 249 " " NAG B2002 " - " ASN B 213 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 147.2 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 13 sheets defined 18.0% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.765A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.577A pdb=" N ILE A 378 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.541A pdb=" N GLN A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'B' and resid 143 through 147 removed outlier: 4.130A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 147' Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.549A pdb=" N CYS B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 299 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 477 through 491 removed outlier: 5.581A pdb=" N ASP B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.546A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.355A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 371 removed outlier: 5.867A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 599 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 383 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AA5, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA7, first strand: chain 'A' and resid 868 through 869 removed outlier: 6.709A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 868 through 869 removed outlier: 7.112A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB1, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 199 Processing sheet with id=AB3, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB4, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.573A pdb=" N VAL B 271 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY B 282 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 273 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 372 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: 0.53 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1492 1.34 - 1.46: 1220 1.46 - 1.59: 1932 1.59 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 4696 Sorted by residual: bond pdb=" N ASP A 511 " pdb=" CA ASP A 511 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.60e+00 bond pdb=" C ASP A 514 " pdb=" N TRP A 515 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.42e-02 4.96e+03 4.53e+00 bond pdb=" N HIS A 512 " pdb=" CA HIS A 512 " ideal model delta sigma weight residual 1.464 1.488 -0.024 1.20e-02 6.94e+03 4.03e+00 bond pdb=" N PRO A 510B" pdb=" CA PRO A 510B" ideal model delta sigma weight residual 1.472 1.494 -0.022 1.32e-02 5.74e+03 2.76e+00 bond pdb=" N PRO A 510B" pdb=" CD PRO A 510B" ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.53e+00 ... (remaining 4691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 6129 1.11 - 2.23: 233 2.23 - 3.34: 49 3.34 - 4.46: 11 4.46 - 5.57: 2 Bond angle restraints: 6424 Sorted by residual: angle pdb=" C SER A 510A" pdb=" N PRO A 510B" pdb=" CA PRO A 510B" ideal model delta sigma weight residual 119.05 124.04 -4.99 1.11e+00 8.12e-01 2.02e+01 angle pdb=" CA ASP A 511 " pdb=" C ASP A 511 " pdb=" O ASP A 511 " ideal model delta sigma weight residual 120.55 116.86 3.69 1.06e+00 8.90e-01 1.21e+01 angle pdb=" CA ASP A 511 " pdb=" C ASP A 511 " pdb=" N HIS A 512 " ideal model delta sigma weight residual 117.30 120.01 -2.71 1.16e+00 7.43e-01 5.45e+00 angle pdb=" C HIS A 512 " pdb=" CA HIS A 512 " pdb=" CB HIS A 512 " ideal model delta sigma weight residual 111.40 108.49 2.91 1.29e+00 6.01e-01 5.10e+00 angle pdb=" CA ASN B 249 " pdb=" CB ASN B 249 " pdb=" CG ASN B 249 " ideal model delta sigma weight residual 112.60 114.85 -2.25 1.00e+00 1.00e+00 5.08e+00 ... (remaining 6419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 2590 14.53 - 29.07: 167 29.07 - 43.60: 43 43.60 - 58.13: 18 58.13 - 72.67: 4 Dihedral angle restraints: 2822 sinusoidal: 991 harmonic: 1831 Sorted by residual: dihedral pdb=" CB CYS B 281 " pdb=" SG CYS B 281 " pdb=" SG CYS B 297 " pdb=" CB CYS B 297 " ideal model delta sinusoidal sigma weight residual 93.00 151.47 -58.47 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS A 466 " pdb=" SG CYS A 466 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual -86.00 -125.92 39.92 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 588 " pdb=" CB CYS A 588 " ideal model delta sinusoidal sigma weight residual -86.00 -119.04 33.04 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 2819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 450 0.038 - 0.075: 171 0.075 - 0.112: 76 0.112 - 0.150: 13 0.150 - 0.187: 1 Chirality restraints: 711 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 355 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA HIS A 512 " pdb=" N HIS A 512 " pdb=" C HIS A 512 " pdb=" CB HIS A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 708 not shown) Planarity restraints: 841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 249 " -0.027 2.00e-02 2.50e+03 2.56e-02 8.19e+00 pdb=" CG ASN B 249 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 249 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 249 " 0.031 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 510B" 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C PRO A 510B" -0.026 2.00e-02 2.50e+03 pdb=" O PRO A 510B" 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 511 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 287 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 288 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.017 5.00e-02 4.00e+02 ... (remaining 838 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1241 2.81 - 3.33: 3705 3.33 - 3.85: 7265 3.85 - 4.38: 8555 4.38 - 4.90: 15378 Nonbonded interactions: 36144 Sorted by model distance: nonbonded pdb=" OE1 GLU B 289 " pdb=" NZ LYS B 350 " model vdw 2.281 3.120 nonbonded pdb=" NZ LYS B 211 " pdb=" OH TYR B 226 " model vdw 2.348 3.120 nonbonded pdb=" NZ LYS B 191 " pdb=" O MET B 488 " model vdw 2.368 3.120 nonbonded pdb=" OG SER B 272 " pdb=" ND1 HIS B 279 " model vdw 2.416 3.120 nonbonded pdb=" OD1 ASN B 247 " pdb=" N LEU B 248 " model vdw 2.418 3.120 ... (remaining 36139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.460 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.004 0.030 4720 Z= 0.167 Angle : 0.558 9.236 6478 Z= 0.301 Chirality : 0.047 0.187 711 Planarity : 0.004 0.030 835 Dihedral : 11.370 72.668 1590 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.28 % Allowed : 4.21 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.11 (0.34), residues: 620 helix: -1.49 (0.52), residues: 85 sheet: 0.25 (0.41), residues: 165 loop : 0.27 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 587 TYR 0.015 0.002 TYR B 414 PHE 0.015 0.001 PHE A 594 TRP 0.011 0.002 TRP A 444 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 4696) covalent geometry : angle 0.53556 / 0.30 ( 6424) SS BOND : bond 0.00328 / 0.18 ( 18) SS BOND : angle 0.69498 / 0.53 ( 36) hydrogen bonds : bond 0.15836 / 10.10 ( 143) hydrogen bonds : angle 7.36673 / 5.36 ( 372) link_NAG-ASN : bond 0.00330 / 0.18 ( 6) link_NAG-ASN : angle 2.96289 / 1.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.173 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.1382 time to fit residues: 6.8360 Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122419 restraints weight = 5415.285| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.18 r_work: 0.3232 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4720 Z= 0.161 Angle : 0.530 6.806 6478 Z= 0.275 Chirality : 0.047 0.156 711 Planarity : 0.004 0.038 835 Dihedral : 5.304 57.989 804 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.84 % Allowed : 5.34 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.09 (0.34), residues: 620 helix: -1.17 (0.56), residues: 80 sheet: 0.10 (0.41), residues: 159 loop : 0.25 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 587 TYR 0.013 0.002 TYR A 426 PHE 0.017 0.001 PHE A 594 TRP 0.015 0.001 TRP A 444 HIS 0.006 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 4696) covalent geometry : angle 0.52019 / 0.27 ( 6424) SS BOND : bond 0.00322 / 0.21 ( 18) SS BOND : angle 0.67825 / 0.50 ( 36) hydrogen bonds : bond 0.03686 / 2.49 ( 143) hydrogen bonds : angle 6.05556 / 4.43 ( 372) link_NAG-ASN : bond 0.00375 / 0.20 ( 6) link_NAG-ASN : angle 1.84688 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.113 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.1327 time to fit residues: 6.8468 Evaluate side-chains 43 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121262 restraints weight = 5405.307| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.18 r_work: 0.3223 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4720 Z= 0.165 Angle : 0.596 15.894 6478 Z= 0.285 Chirality : 0.047 0.170 711 Planarity : 0.004 0.042 835 Dihedral : 5.328 50.078 804 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.12 % Allowed : 6.18 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.25 (0.34), residues: 620 helix: -1.24 (0.56), residues: 80 sheet: -0.02 (0.41), residues: 159 loop : 0.14 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.012 0.001 TYR A 426 PHE 0.017 0.001 PHE A 594 TRP 0.012 0.001 TRP A 444 HIS 0.006 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 4696) covalent geometry : angle 0.53430 / 0.27 ( 6424) SS BOND : bond 0.00302 / 0.21 ( 18) SS BOND : angle 0.59599 / 0.45 ( 36) hydrogen bonds : bond 0.03457 / 2.34 ( 143) hydrogen bonds : angle 5.96352 / 4.37 ( 372) link_NAG-ASN : bond 0.00897 / 0.69 ( 6) link_NAG-ASN : angle 5.00797 / 2.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.181 Fit side-chains REVERT: B 240 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7498 (ttt180) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.1089 time to fit residues: 5.1471 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120218 restraints weight = 5441.981| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.30 r_work: 0.3208 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4720 Z= 0.161 Angle : 0.580 14.078 6478 Z= 0.281 Chirality : 0.047 0.177 711 Planarity : 0.004 0.043 835 Dihedral : 4.834 50.886 804 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.69 % Allowed : 6.74 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.28 (0.34), residues: 620 helix: -1.17 (0.57), residues: 75 sheet: -0.10 (0.41), residues: 159 loop : 0.10 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 413 TYR 0.012 0.001 TYR A 426 PHE 0.016 0.001 PHE A 594 TRP 0.012 0.001 TRP A 444 HIS 0.006 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 4696) covalent geometry : angle 0.52631 / 0.27 ( 6424) SS BOND : bond 0.00319 / 0.21 ( 18) SS BOND : angle 0.90012 / 0.58 ( 36) hydrogen bonds : bond 0.03344 / 2.29 ( 143) hydrogen bonds : angle 5.98871 / 4.46 ( 372) link_NAG-ASN : bond 0.00733 / 0.55 ( 6) link_NAG-ASN : angle 4.53190 / 2.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.166 Fit side-chains REVERT: B 240 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7476 (ttt180) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.1248 time to fit residues: 5.8313 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122179 restraints weight = 5434.541| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.19 r_work: 0.3235 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4720 Z= 0.129 Angle : 0.538 11.301 6478 Z= 0.260 Chirality : 0.047 0.256 711 Planarity : 0.003 0.044 835 Dihedral : 4.740 50.988 804 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 6.46 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.18 (0.34), residues: 620 helix: -1.11 (0.59), residues: 75 sheet: -0.03 (0.41), residues: 153 loop : 0.17 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 413 TYR 0.010 0.001 TYR A 426 PHE 0.014 0.001 PHE A 594 TRP 0.015 0.001 TRP A 444 HIS 0.004 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 4696) covalent geometry : angle 0.50084 / 0.25 ( 6424) SS BOND : bond 0.00246 / 0.16 ( 18) SS BOND : angle 0.66746 / 0.45 ( 36) hydrogen bonds : bond 0.03116 / 2.13 ( 143) hydrogen bonds : angle 5.70403 / 4.24 ( 372) link_NAG-ASN : bond 0.00738 / 0.51 ( 6) link_NAG-ASN : angle 3.69822 / 2.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.166 Fit side-chains REVERT: A 455 LEU cc_start: 0.7414 (mt) cc_final: 0.7214 (mt) REVERT: B 240 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7480 (ttt180) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1144 time to fit residues: 5.5601 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 43 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121804 restraints weight = 5482.806| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.38 r_work: 0.3224 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4720 Z= 0.111 Angle : 0.545 9.814 6478 Z= 0.261 Chirality : 0.047 0.268 711 Planarity : 0.003 0.043 835 Dihedral : 4.930 50.716 804 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.69 % Allowed : 7.02 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.12 (0.34), residues: 620 helix: -1.12 (0.58), residues: 75 sheet: 0.03 (0.42), residues: 153 loop : 0.22 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 413 TYR 0.008 0.001 TYR A 426 PHE 0.013 0.001 PHE A 594 TRP 0.013 0.001 TRP A 444 HIS 0.004 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4696) covalent geometry : angle 0.49499 / 0.25 ( 6424) SS BOND : bond 0.00203 / 0.14 ( 18) SS BOND : angle 0.55902 / 0.39 ( 36) hydrogen bonds : bond 0.03067 / 2.07 ( 143) hydrogen bonds : angle 5.57341 / 4.14 ( 372) link_NAG-ASN : bond 0.00651 / 0.42 ( 6) link_NAG-ASN : angle 4.35242 / 2.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.174 Fit side-chains REVERT: A 371 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7321 (t0) REVERT: B 187 ASP cc_start: 0.8187 (m-30) cc_final: 0.7903 (m-30) REVERT: B 240 ARG cc_start: 0.8065 (mtp180) cc_final: 0.7422 (ttt180) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1278 time to fit residues: 6.2503 Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.134494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119806 restraints weight = 5512.324| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.34 r_work: 0.3205 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4720 Z= 0.167 Angle : 0.580 12.084 6478 Z= 0.278 Chirality : 0.047 0.238 711 Planarity : 0.004 0.044 835 Dihedral : 5.076 50.613 804 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 7.02 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.21 (0.34), residues: 620 helix: -1.02 (0.59), residues: 75 sheet: -0.03 (0.41), residues: 159 loop : 0.12 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 413 TYR 0.013 0.001 TYR A 426 PHE 0.016 0.001 PHE A 594 TRP 0.015 0.001 TRP A 444 HIS 0.006 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 4696) covalent geometry : angle 0.52815 / 0.27 ( 6424) SS BOND : bond 0.00312 / 0.22 ( 18) SS BOND : angle 0.64704 / 0.45 ( 36) hydrogen bonds : bond 0.03280 / 2.22 ( 143) hydrogen bonds : angle 5.75317 / 4.25 ( 372) link_NAG-ASN : bond 0.00508 / 0.34 ( 6) link_NAG-ASN : angle 4.55380 / 2.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 187 ASP cc_start: 0.8290 (m-30) cc_final: 0.7920 (m-30) REVERT: B 240 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7458 (ttt180) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.1391 time to fit residues: 6.5556 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117813 restraints weight = 5519.927| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.40 r_work: 0.3179 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4720 Z= 0.176 Angle : 0.600 11.925 6478 Z= 0.287 Chirality : 0.048 0.262 711 Planarity : 0.004 0.045 835 Dihedral : 5.034 50.775 804 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.40 % Allowed : 7.30 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.33 (0.34), residues: 620 helix: -1.10 (0.59), residues: 76 sheet: -0.09 (0.41), residues: 159 loop : 0.02 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 361 TYR 0.013 0.002 TYR A 427 PHE 0.015 0.001 PHE A 594 TRP 0.015 0.001 TRP A 444 HIS 0.006 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 4696) covalent geometry : angle 0.55416 / 0.28 ( 6424) SS BOND : bond 0.00323 / 0.23 ( 18) SS BOND : angle 0.64078 / 0.46 ( 36) hydrogen bonds : bond 0.03348 / 2.27 ( 143) hydrogen bonds : angle 5.88065 / 4.35 ( 372) link_NAG-ASN : bond 0.00659 / 0.40 ( 6) link_NAG-ASN : angle 4.36981 / 2.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: B 240 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7495 (ttt180) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.1380 time to fit residues: 6.0347 Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118746 restraints weight = 5438.497| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.40 r_work: 0.3186 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4720 Z= 0.140 Angle : 0.559 11.809 6478 Z= 0.268 Chirality : 0.047 0.285 711 Planarity : 0.004 0.045 835 Dihedral : 4.900 50.943 804 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.40 % Allowed : 7.87 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.25 (0.34), residues: 620 helix: -1.00 (0.60), residues: 74 sheet: -0.07 (0.41), residues: 153 loop : 0.08 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.011 0.001 TYR A 426 PHE 0.014 0.001 PHE A 594 TRP 0.014 0.001 TRP A 444 HIS 0.005 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4696) covalent geometry : angle 0.51288 / 0.26 ( 6424) SS BOND : bond 0.00246 / 0.17 ( 18) SS BOND : angle 0.56375 / 0.40 ( 36) hydrogen bonds : bond 0.03148 / 2.14 ( 143) hydrogen bonds : angle 5.68809 / 4.22 ( 372) link_NAG-ASN : bond 0.00683 / 0.40 ( 6) link_NAG-ASN : angle 4.21889 / 2.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.203 Fit side-chains REVERT: B 187 ASP cc_start: 0.8329 (m-30) cc_final: 0.7969 (m-30) REVERT: B 240 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7442 (ttt180) outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 0.1309 time to fit residues: 5.6699 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119361 restraints weight = 5442.158| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.41 r_work: 0.3186 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4720 Z= 0.130 Angle : 0.545 11.561 6478 Z= 0.261 Chirality : 0.047 0.291 711 Planarity : 0.004 0.044 835 Dihedral : 4.762 50.606 804 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 8.15 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.22 (0.34), residues: 620 helix: -1.00 (0.60), residues: 74 sheet: -0.06 (0.41), residues: 153 loop : 0.10 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.010 0.001 TYR A 426 PHE 0.014 0.001 PHE A 594 TRP 0.014 0.001 TRP A 444 HIS 0.004 0.001 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4696) covalent geometry : angle 0.50176 / 0.25 ( 6424) SS BOND : bond 0.00229 / 0.16 ( 18) SS BOND : angle 0.53765 / 0.38 ( 36) hydrogen bonds : bond 0.03070 / 2.09 ( 143) hydrogen bonds : angle 5.61885 / 4.17 ( 372) link_NAG-ASN : bond 0.00658 / 0.38 ( 6) link_NAG-ASN : angle 4.05524 / 2.65 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.179 Fit side-chains REVERT: B 187 ASP cc_start: 0.8395 (m-30) cc_final: 0.8027 (m-30) REVERT: B 240 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7471 (ttt180) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1111 time to fit residues: 5.0836 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.0070 overall best weight: 0.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124042 restraints weight = 5423.245| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.42 r_work: 0.3241 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4720 Z= 0.083 Angle : 0.492 11.131 6478 Z= 0.235 Chirality : 0.046 0.305 711 Planarity : 0.003 0.044 835 Dihedral : 4.344 49.339 804 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.12 % Allowed : 8.99 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 0.12 (0.35), residues: 620 helix: -0.49 (0.64), residues: 67 sheet: -0.06 (0.42), residues: 148 loop : 0.37 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 413 TYR 0.007 0.001 TYR A 427 PHE 0.010 0.001 PHE A 594 TRP 0.010 0.001 TRP A 444 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.08 ( 4696) covalent geometry : angle 0.44832 / 0.23 ( 6424) SS BOND : bond 0.00119 / 0.07 ( 18) SS BOND : angle 0.43550 / 0.29 ( 36) hydrogen bonds : bond 0.02752 / 1.88 ( 143) hydrogen bonds : angle 5.20929 / 3.89 ( 372) link_NAG-ASN : bond 0.00659 / 0.38 ( 6) link_NAG-ASN : angle 3.85291 / 2.53 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1478.19 seconds wall clock time: 26 minutes 8.47 seconds (1568.47 seconds total)