Starting phenix.real_space_refine on Thu Oct 22 19:16:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukn_20807/10_2026/6ukn_20807.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 S 40 5.16 5 Cl 1 4.86 5 C 2689 2.51 5 N 639 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4109 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4029 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 514} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.78, per 1000 atoms: 0.19 Number of scatterers: 4109 At special positions: 0 Unit cell: (93.234, 68.22, 94.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 Cl 1 17.00 S 40 16.00 O 739 8.00 N 639 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 352 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 312 " " NAG C 1 " - " ASN A 360 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 128.8 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 66.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.599A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.286A pdb=" N PHE A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.852A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.629A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 Processing helix chain 'A' and resid 239 through 269 removed outlier: 4.421A pdb=" N ALA A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.579A pdb=" N VAL A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 421 through 428 removed outlier: 4.156A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.752A pdb=" N LEU A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 452 - end of helix removed outlier: 3.942A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.783A pdb=" N ARG A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 504 through 536 removed outlier: 3.952A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.870A pdb=" N ASP A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 4.038A pdb=" N GLN A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.842A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.696A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 4.425A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 4.034A pdb=" N PHE A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 309 removed outlier: 4.046A pdb=" N ILE A 305 " --> pdb=" O GLY A 366 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 711 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: 0.31 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1233 1.35 - 1.47: 1103 1.47 - 1.59: 1805 1.59 - 1.71: 0 1.71 - 1.84: 60 Bond restraints: 4201 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" CG1 ILE A 221 " pdb=" CD1 ILE A 221 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 bond pdb=" C PHE A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.08e-02 8.57e+03 1.39e+00 ... (remaining 4196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 5477 1.84 - 3.67: 201 3.67 - 5.51: 33 5.51 - 7.34: 11 7.34 - 9.18: 1 Bond angle restraints: 5723 Sorted by residual: angle pdb=" C ASP A 484 " pdb=" N LYS A 485 " pdb=" CA LYS A 485 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" C LYS A 325 " pdb=" N MET A 326 " pdb=" CA MET A 326 " ideal model delta sigma weight residual 120.82 127.52 -6.70 1.50e+00 4.44e-01 2.00e+01 angle pdb=" C PHE A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" C VAL A 400 " pdb=" N SER A 401 " pdb=" CA SER A 401 " ideal model delta sigma weight residual 122.35 126.42 -4.07 1.46e+00 4.69e-01 7.79e+00 angle pdb=" C ALA A 350 " pdb=" N THR A 351 " pdb=" CA THR A 351 " ideal model delta sigma weight residual 122.46 126.36 -3.90 1.41e+00 5.03e-01 7.64e+00 ... (remaining 5718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2143 17.16 - 34.32: 203 34.32 - 51.48: 43 51.48 - 68.64: 2 68.64 - 85.79: 4 Dihedral angle restraints: 2395 sinusoidal: 869 harmonic: 1526 Sorted by residual: dihedral pdb=" CA LYS A 325 " pdb=" C LYS A 325 " pdb=" N MET A 326 " pdb=" CA MET A 326 " ideal model delta harmonic sigma weight residual 180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLN A 327 " pdb=" C GLN A 327 " pdb=" N VAL A 328 " pdb=" CA VAL A 328 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 2392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 671 0.113 - 0.226: 26 0.226 - 0.339: 3 0.339 - 0.452: 0 0.452 - 0.564: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.27e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.13e+01 ... (remaining 698 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 604 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 605 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 626 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C CYS A 626 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 626 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 627 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 428 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 429 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1459 2.85 - 3.42: 4729 3.42 - 4.00: 7005 4.00 - 4.57: 10048 4.57 - 5.14: 14405 Nonbonded interactions: 37646 Sorted by model distance: nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 511 " pdb=" OG1 THR A 515 " model vdw 2.302 3.040 nonbonded pdb=" O4 BMA B 3 " pdb=" O6 BMA B 3 " model vdw 2.347 3.040 nonbonded pdb=" OD2 ASP A 415 " pdb=" NZ LYS A 485 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 231 " pdb=" OG SER A 231 " model vdw 2.407 3.040 ... (remaining 37641 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 0.180 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.006 0.066 4210 Z= 0.259 Angle : 1.138 26.037 5747 Z= 0.517 Chirality : 0.055 0.564 701 Planarity : 0.006 0.066 694 Dihedral : 13.774 85.794 1416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.47 % Allowed : 9.53 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.33), residues: 534 helix: -0.93 (0.25), residues: 333 sheet: -2.49 (1.44), residues: 10 loop : -3.02 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 528 TYR 0.011 0.001 TYR A 186 PHE 0.016 0.002 PHE A 428 TRP 0.009 0.001 TRP A 505 HIS 0.004 0.002 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 ( 4201) covalent geometry : angle 0.83135 / 0.45 ( 5723) SS BOND : bond 0.00630 / 0.33 ( 3) SS BOND : angle 1.91657 / 1.02 ( 6) hydrogen bonds : bond 0.14098 / 9.38 ( 240) hydrogen bonds : angle 5.36859 / 3.99 ( 711) link_BETA1-4 : bond 0.06482 / 3.25 ( 4) link_BETA1-4 : angle 15.15885 / 7.87 ( 12) link_NAG-ASN : bond 0.02339 / 1.11 ( 2) link_NAG-ASN : angle 10.86311 / 5.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 171 MET cc_start: 0.7574 (ttm) cc_final: 0.6959 (ttm) REVERT: A 279 VAL cc_start: 0.9342 (t) cc_final: 0.8915 (p) REVERT: A 435 MET cc_start: 0.8319 (mmt) cc_final: 0.7700 (mmt) REVERT: A 521 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 547 HIS cc_start: 0.7428 (m170) cc_final: 0.7073 (m170) REVERT: A 559 LEU cc_start: 0.8698 (tp) cc_final: 0.8481 (tp) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.0343 time to fit residues: 5.6215 Evaluate side-chains 85 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30] chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102780 restraints weight = 8311.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105984 restraints weight = 4205.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108179 restraints weight = 2642.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109513 restraints weight = 1929.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110616 restraints weight = 1578.321| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4210 Z= 0.177 Angle : 0.777 18.159 5747 Z= 0.373 Chirality : 0.047 0.460 701 Planarity : 0.005 0.057 694 Dihedral : 5.137 25.244 571 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.49 % Allowed : 17.91 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.36), residues: 534 helix: 0.31 (0.28), residues: 332 sheet: -2.03 (1.65), residues: 10 loop : -2.81 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.011 0.001 TYR A 186 PHE 0.014 0.001 PHE A 428 TRP 0.012 0.001 TRP A 505 HIS 0.003 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 4201) covalent geometry : angle 0.70681 / 0.36 ( 5723) SS BOND : bond 0.01122 / 0.59 ( 3) SS BOND : angle 1.99027 / 1.10 ( 6) hydrogen bonds : bond 0.05160 / 3.45 ( 240) hydrogen bonds : angle 4.39097 / 3.25 ( 711) link_BETA1-4 : bond 0.00553 / 0.27 ( 4) link_BETA1-4 : angle 2.44102 / 1.44 ( 12) link_NAG-ASN : bond 0.01762 / 0.84 ( 2) link_NAG-ASN : angle 9.24693 / 4.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.133 Fit side-chains REVERT: A 224 PHE cc_start: 0.8438 (t80) cc_final: 0.8236 (t80) REVERT: A 262 MET cc_start: 0.8837 (mmm) cc_final: 0.8569 (mmm) REVERT: A 385 ASP cc_start: 0.8553 (t0) cc_final: 0.8351 (t0) REVERT: A 521 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 547 HIS cc_start: 0.7460 (m170) cc_final: 0.7105 (m170) REVERT: A 583 MET cc_start: 0.7797 (tmm) cc_final: 0.7528 (tmm) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.0403 time to fit residues: 6.3203 Evaluate side-chains 94 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [4, 43, 14, 21, 24, 1, 39, 9, 11, 52, 31] chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103601 restraints weight = 8273.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106794 restraints weight = 4217.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109022 restraints weight = 2655.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110489 restraints weight = 1931.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111315 restraints weight = 1561.602| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4210 Z= 0.139 Angle : 0.709 17.942 5747 Z= 0.336 Chirality : 0.044 0.452 701 Planarity : 0.004 0.052 694 Dihedral : 4.823 22.983 571 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.35 % Allowed : 20.70 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.37), residues: 534 helix: 1.05 (0.29), residues: 325 sheet: -1.45 (1.73), residues: 10 loop : -2.77 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 603 TYR 0.012 0.001 TYR A 614 PHE 0.014 0.001 PHE A 154 TRP 0.016 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4201) covalent geometry : angle 0.63986 / 0.32 ( 5723) SS BOND : bond 0.00629 / 0.33 ( 3) SS BOND : angle 1.48943 / 0.81 ( 6) hydrogen bonds : bond 0.04716 / 3.14 ( 240) hydrogen bonds : angle 3.98827 / 2.94 ( 711) link_BETA1-4 : bond 0.00530 / 0.26 ( 4) link_BETA1-4 : angle 1.94926 / 1.17 ( 12) link_NAG-ASN : bond 0.01802 / 0.86 ( 2) link_NAG-ASN : angle 8.98018 / 4.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.146 Fit side-chains REVERT: A 171 MET cc_start: 0.8082 (ttp) cc_final: 0.7158 (ttm) REVERT: A 262 MET cc_start: 0.8764 (mmm) cc_final: 0.8558 (mmm) REVERT: A 521 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 547 HIS cc_start: 0.7455 (m170) cc_final: 0.6962 (m90) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.0463 time to fit residues: 7.2370 Evaluate side-chains 102 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [30, 50, 10, 32, 14, 48, 27, 24, 17, 13, 22] chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 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 = 0.3559 r_free = 0.3559 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106484 restraints weight = 8181.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109425 restraints weight = 4344.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111439 restraints weight = 2838.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112766 restraints weight = 2130.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113499 restraints weight = 1764.910| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4210 Z= 0.146 Angle : 0.721 17.860 5747 Z= 0.342 Chirality : 0.045 0.450 701 Planarity : 0.004 0.054 694 Dihedral : 4.832 26.706 571 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.72 % Allowed : 23.02 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.38), residues: 534 helix: 1.34 (0.30), residues: 328 sheet: -1.37 (1.74), residues: 10 loop : -2.77 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 603 TYR 0.011 0.001 TYR A 186 PHE 0.012 0.001 PHE A 428 TRP 0.015 0.001 TRP A 635 HIS 0.001 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4201) covalent geometry : angle 0.65505 / 0.33 ( 5723) SS BOND : bond 0.00670 / 0.35 ( 3) SS BOND : angle 1.68172 / 0.92 ( 6) hydrogen bonds : bond 0.04586 / 3.06 ( 240) hydrogen bonds : angle 3.95934 / 2.92 ( 711) link_BETA1-4 : bond 0.00549 / 0.27 ( 4) link_BETA1-4 : angle 1.83679 / 1.12 ( 12) link_NAG-ASN : bond 0.01762 / 0.84 ( 2) link_NAG-ASN : angle 8.91159 / 4.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.150 Fit side-chains REVERT: A 385 ASP cc_start: 0.8431 (t0) cc_final: 0.8054 (t0) REVERT: A 435 MET cc_start: 0.8433 (mmt) cc_final: 0.8107 (mmt) REVERT: A 521 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 547 HIS cc_start: 0.7407 (m170) cc_final: 0.6965 (m90) REVERT: A 583 MET cc_start: 0.7445 (tmm) cc_final: 0.7216 (tmm) REVERT: A 587 MET cc_start: 0.7812 (ttp) cc_final: 0.7521 (ttm) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.0437 time to fit residues: 6.4505 Evaluate side-chains 99 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [27, 20, 19, 31, 26, 48, 22, 25, 30, 15, 2] chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 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 = 0.3561 r_free = 0.3561 target = 0.125334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106045 restraints weight = 8116.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109143 restraints weight = 4246.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111260 restraints weight = 2735.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112561 restraints weight = 2034.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113517 restraints weight = 1685.907| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4210 Z= 0.135 Angle : 0.686 17.696 5747 Z= 0.325 Chirality : 0.044 0.451 701 Planarity : 0.004 0.052 694 Dihedral : 4.638 23.944 571 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.95 % Allowed : 24.42 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.38), residues: 534 helix: 1.51 (0.30), residues: 326 sheet: -1.23 (1.77), residues: 10 loop : -2.74 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 603 TYR 0.010 0.001 TYR A 186 PHE 0.011 0.001 PHE A 154 TRP 0.016 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4201) covalent geometry : angle 0.61701 / 0.31 ( 5723) SS BOND : bond 0.00708 / 0.37 ( 3) SS BOND : angle 1.79030 / 0.98 ( 6) hydrogen bonds : bond 0.04402 / 2.94 ( 240) hydrogen bonds : angle 3.81408 / 2.82 ( 711) link_BETA1-4 : bond 0.00533 / 0.26 ( 4) link_BETA1-4 : angle 1.72739 / 1.08 ( 12) link_NAG-ASN : bond 0.01754 / 0.84 ( 2) link_NAG-ASN : angle 8.82059 / 4.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 521 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 547 HIS cc_start: 0.7506 (m170) cc_final: 0.6983 (m90) REVERT: A 583 MET cc_start: 0.7476 (tmm) cc_final: 0.7190 (tmm) REVERT: A 587 MET cc_start: 0.7914 (ttp) cc_final: 0.7574 (ttm) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.0429 time to fit residues: 6.3858 Evaluate side-chains 102 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [26, 11, 33, 10, 17, 49, 1, 15, 32, 30, 0] chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107926 restraints weight = 8374.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110916 restraints weight = 4424.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112981 restraints weight = 2880.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113966 restraints weight = 2159.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115055 restraints weight = 1835.888| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4210 Z= 0.121 Angle : 0.671 17.508 5747 Z= 0.316 Chirality : 0.043 0.452 701 Planarity : 0.004 0.049 694 Dihedral : 4.473 22.007 571 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.42 % Allowed : 24.88 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.39), residues: 534 helix: 1.73 (0.30), residues: 326 sheet: -0.87 (1.81), residues: 10 loop : -2.67 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.010 0.001 TYR A 272 PHE 0.011 0.001 PHE A 154 TRP 0.017 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4201) covalent geometry : angle 0.60334 / 0.30 ( 5723) SS BOND : bond 0.00532 / 0.28 ( 3) SS BOND : angle 1.52269 / 0.84 ( 6) hydrogen bonds : bond 0.04114 / 2.78 ( 240) hydrogen bonds : angle 3.67296 / 2.71 ( 711) link_BETA1-4 : bond 0.00517 / 0.26 ( 4) link_BETA1-4 : angle 1.63001 / 1.04 ( 12) link_NAG-ASN : bond 0.01788 / 0.85 ( 2) link_NAG-ASN : angle 8.70731 / 4.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 297 LYS cc_start: 0.8448 (mptt) cc_final: 0.7865 (tmtt) REVERT: A 385 ASP cc_start: 0.8332 (t0) cc_final: 0.8069 (t0) REVERT: A 521 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 547 HIS cc_start: 0.7512 (m170) cc_final: 0.7014 (m90) REVERT: A 583 MET cc_start: 0.7498 (tmm) cc_final: 0.7228 (tmm) outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.0423 time to fit residues: 7.0469 Evaluate side-chains 105 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [7, 23, 0, 46, 29, 35, 48, 16, 41, 4, 18] chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 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 = 0.3581 r_free = 0.3581 target = 0.126518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107360 restraints weight = 8274.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110419 restraints weight = 4358.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112539 restraints weight = 2817.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113787 restraints weight = 2090.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114814 restraints weight = 1734.322| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4210 Z= 0.131 Angle : 0.688 17.480 5747 Z= 0.322 Chirality : 0.044 0.465 701 Planarity : 0.004 0.049 694 Dihedral : 4.432 20.604 571 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.72 % Allowed : 26.74 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.39), residues: 534 helix: 1.77 (0.30), residues: 327 sheet: -0.72 (1.84), residues: 10 loop : -2.62 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 608 TYR 0.009 0.001 TYR A 272 PHE 0.011 0.001 PHE A 428 TRP 0.018 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4201) covalent geometry : angle 0.62371 / 0.31 ( 5723) SS BOND : bond 0.00402 / 0.21 ( 3) SS BOND : angle 1.55501 / 0.86 ( 6) hydrogen bonds : bond 0.04137 / 2.79 ( 240) hydrogen bonds : angle 3.70877 / 2.75 ( 711) link_BETA1-4 : bond 0.00533 / 0.27 ( 4) link_BETA1-4 : angle 1.58628 / 1.00 ( 12) link_NAG-ASN : bond 0.01664 / 0.79 ( 2) link_NAG-ASN : angle 8.64605 / 4.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.091 Fit side-chains REVERT: A 262 MET cc_start: 0.8872 (tpp) cc_final: 0.8489 (mmm) REVERT: A 521 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 547 HIS cc_start: 0.7545 (m170) cc_final: 0.7016 (m90) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.0421 time to fit residues: 6.3777 Evaluate side-chains 103 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [1, 47, 37, 27, 36, 17, 7, 29, 28, 52, 21] chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 27 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108453 restraints weight = 8162.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111486 restraints weight = 4422.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113518 restraints weight = 2903.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114774 restraints weight = 2180.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115714 restraints weight = 1817.850| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4210 Z= 0.125 Angle : 0.728 17.386 5747 Z= 0.332 Chirality : 0.045 0.467 701 Planarity : 0.004 0.049 694 Dihedral : 4.345 22.596 571 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.02 % Allowed : 27.67 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.39), residues: 534 helix: 1.76 (0.30), residues: 327 sheet: -0.72 (1.79), residues: 10 loop : -2.58 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.009 0.001 TYR A 272 PHE 0.010 0.001 PHE A 428 TRP 0.019 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4201) covalent geometry : angle 0.66792 / 0.32 ( 5723) SS BOND : bond 0.00499 / 0.26 ( 3) SS BOND : angle 1.68790 / 0.94 ( 6) hydrogen bonds : bond 0.04038 / 2.72 ( 240) hydrogen bonds : angle 3.71833 / 2.76 ( 711) link_BETA1-4 : bond 0.00508 / 0.25 ( 4) link_BETA1-4 : angle 1.56671 / 1.00 ( 12) link_NAG-ASN : bond 0.01691 / 0.81 ( 2) link_NAG-ASN : angle 8.60569 / 4.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 262 MET cc_start: 0.8851 (tpp) cc_final: 0.8461 (mmm) REVERT: A 358 GLN cc_start: 0.7493 (tt0) cc_final: 0.7229 (tt0) REVERT: A 521 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 13 outliers final: 12 residues processed: 104 average time/residue: 0.0444 time to fit residues: 6.4577 Evaluate side-chains 102 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [0, 7, 38, 25, 2, 16, 31, 50, 24, 48, 10] chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 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 = 0.3586 r_free = 0.3586 target = 0.127047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108013 restraints weight = 8235.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110941 restraints weight = 4416.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112972 restraints weight = 2894.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114127 restraints weight = 2168.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115207 restraints weight = 1820.962| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4210 Z= 0.138 Angle : 0.770 19.682 5747 Z= 0.347 Chirality : 0.044 0.327 701 Planarity : 0.004 0.050 694 Dihedral : 4.347 22.255 571 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.95 % Allowed : 27.91 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.39), residues: 534 helix: 1.74 (0.30), residues: 327 sheet: -0.64 (1.84), residues: 10 loop : -2.52 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.008 0.001 TYR A 186 PHE 0.012 0.001 PHE A 428 TRP 0.019 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4201) covalent geometry : angle 0.69752 / 0.33 ( 5723) SS BOND : bond 0.00523 / 0.27 ( 3) SS BOND : angle 1.69290 / 0.94 ( 6) hydrogen bonds : bond 0.04114 / 2.75 ( 240) hydrogen bonds : angle 3.82180 / 2.82 ( 711) link_BETA1-4 : bond 0.00511 / 0.25 ( 4) link_BETA1-4 : angle 1.62631 / 1.02 ( 12) link_NAG-ASN : bond 0.01139 / 0.54 ( 2) link_NAG-ASN : angle 9.78000 / 5.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.148 Fit side-chains REVERT: A 262 MET cc_start: 0.8866 (tpp) cc_final: 0.8490 (mmm) REVERT: A 358 GLN cc_start: 0.7504 (tt0) cc_final: 0.7238 (tt0) REVERT: A 520 LEU cc_start: 0.9162 (mt) cc_final: 0.8810 (mt) REVERT: A 521 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8576 (tm-30) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.0442 time to fit residues: 6.5073 Evaluate side-chains 105 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [51, 15, 21, 25, 37, 30, 22, 3, 10, 0, 27] chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.0020 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 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 = 0.3600 r_free = 0.3600 target = 0.127824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109449 restraints weight = 7850.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112384 restraints weight = 4272.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114371 restraints weight = 2803.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115514 restraints weight = 2090.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116274 restraints weight = 1743.534| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4210 Z= 0.129 Angle : 0.769 18.954 5747 Z= 0.347 Chirality : 0.044 0.312 701 Planarity : 0.004 0.051 694 Dihedral : 4.314 22.072 571 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.26 % Allowed : 27.91 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.39), residues: 534 helix: 1.76 (0.30), residues: 327 sheet: -0.64 (1.81), residues: 10 loop : -2.50 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 117 TYR 0.006 0.001 TYR A 186 PHE 0.009 0.001 PHE A 428 TRP 0.020 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4201) covalent geometry : angle 0.69940 / 0.33 ( 5723) SS BOND : bond 0.00473 / 0.25 ( 3) SS BOND : angle 1.55191 / 0.87 ( 6) hydrogen bonds : bond 0.03979 / 2.67 ( 240) hydrogen bonds : angle 3.77331 / 2.79 ( 711) link_BETA1-4 : bond 0.00505 / 0.25 ( 4) link_BETA1-4 : angle 1.55911 / 1.01 ( 12) link_NAG-ASN : bond 0.01559 / 0.74 ( 2) link_NAG-ASN : angle 9.64535 / 5.04 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.086 Fit side-chains REVERT: A 262 MET cc_start: 0.8857 (tpp) cc_final: 0.8474 (mmm) REVERT: A 358 GLN cc_start: 0.7559 (tt0) cc_final: 0.7295 (tt0) REVERT: A 520 LEU cc_start: 0.9176 (mt) cc_final: 0.8828 (mt) REVERT: A 521 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8594 (tm-30) outliers start: 14 outliers final: 13 residues processed: 104 average time/residue: 0.0356 time to fit residues: 5.3902 Evaluate side-chains 103 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: [9, 3, 14, 50, 27, 34, 11, 2, 23, 10, 52] chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 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 = 0.3591 r_free = 0.3591 target = 0.127197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108899 restraints weight = 7921.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111688 restraints weight = 4260.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113712 restraints weight = 2813.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114473 restraints weight = 2099.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115682 restraints weight = 1806.099| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4210 Z= 0.138 Angle : 0.776 19.067 5747 Z= 0.349 Chirality : 0.043 0.331 701 Planarity : 0.004 0.052 694 Dihedral : 4.307 21.878 571 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.02 % Allowed : 28.84 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.39), residues: 534 helix: 1.75 (0.30), residues: 327 sheet: -0.75 (1.80), residues: 10 loop : -2.43 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 117 TYR 0.006 0.001 TYR A 272 PHE 0.011 0.001 PHE A 428 TRP 0.020 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4201) covalent geometry : angle 0.70764 / 0.33 ( 5723) SS BOND : bond 0.00497 / 0.26 ( 3) SS BOND : angle 1.62885 / 0.91 ( 6) hydrogen bonds : bond 0.04050 / 2.71 ( 240) hydrogen bonds : angle 3.80572 / 2.79 ( 711) link_BETA1-4 : bond 0.00524 / 0.26 ( 4) link_BETA1-4 : angle 1.58262 / 1.01 ( 12) link_NAG-ASN : bond 0.01600 / 0.76 ( 2) link_NAG-ASN : angle 9.54471 / 4.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 755.25 seconds wall clock time: 13 minutes 44.10 seconds (824.10 seconds total)