Starting phenix.real_space_refine on Tue Feb 11 05:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_20807.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_20807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_20807.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_20807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukn_20807/02_2025/6ukn_20807.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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 dihedrals: 9 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 dihedrals: 9 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: 3.05, per 1000 atoms: 0.74 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: 1.18 Conformation dependent library (CDL) restraints added in 472.1 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: 0.34 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: 1.01 Time building geometry restraints manager: 1.30 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 - 22.88: 2316 22.88 - 45.75: 147 45.75 - 68.63: 10 68.63 - 91.51: 28 91.51 - 114.38: 16 Dihedral angle restraints: 2517 sinusoidal: 991 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 2514 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: 0.400 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4201 Z= 0.346 Angle : 0.831 9.175 5723 Z= 0.447 Chirality : 0.055 0.564 701 Planarity : 0.006 0.066 694 Dihedral : 20.626 114.383 1538 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A 505 HIS 0.004 0.002 HIS A 615 PHE 0.016 0.002 PHE A 428 TYR 0.011 0.001 TYR A 186 ARG 0.001 0.000 ARG A 528 *********************** 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 : 0.457 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: 0.8320 (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: 0.1437 time to fit residues: 22.7535 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3528 r_free = 0.3528 target = 0.122725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103314 restraints weight = 8185.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106516 restraints weight = 4122.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108724 restraints weight = 2591.961| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4201 Z= 0.259 Angle : 0.740 7.980 5723 Z= 0.362 Chirality : 0.048 0.459 701 Planarity : 0.005 0.056 694 Dihedral : 18.211 100.829 693 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.26 % Allowed : 18.37 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.36), residues: 534 helix: 0.38 (0.28), residues: 331 sheet: -1.94 (1.66), residues: 10 loop : -2.84 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.003 0.001 HIS A 615 PHE 0.014 0.001 PHE A 428 TYR 0.011 0.001 TYR A 186 ARG 0.002 0.000 ARG A 603 *********************** 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 120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.440 Fit side-chains REVERT: A 262 MET cc_start: 0.8854 (mmm) cc_final: 0.8570 (mmm) REVERT: A 385 ASP cc_start: 0.8587 (t0) cc_final: 0.8367 (t0) REVERT: A 521 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 547 HIS cc_start: 0.7471 (m170) cc_final: 0.7108 (m170) REVERT: A 583 MET cc_start: 0.7617 (tmm) cc_final: 0.7182 (tmm) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.1026 time to fit residues: 15.8651 Evaluate side-chains 98 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 602 LEU Chi-restraints excluded: chain A residue 604 THR 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: chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3547 r_free = 0.3547 target = 0.124038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104488 restraints weight = 8137.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107694 restraints weight = 4174.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109892 restraints weight = 2632.994| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4201 Z= 0.186 Angle : 0.686 7.668 5723 Z= 0.328 Chirality : 0.048 0.478 701 Planarity : 0.004 0.053 694 Dihedral : 15.515 95.187 693 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.12 % Allowed : 20.47 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.37), residues: 534 helix: 1.09 (0.29), residues: 325 sheet: -1.47 (1.71), residues: 10 loop : -2.76 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.000 0.000 HIS A 547 PHE 0.014 0.001 PHE A 154 TYR 0.010 0.001 TYR A 614 ARG 0.001 0.000 ARG A 603 *********************** 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: 22 poor density : 101 time to evaluate : 0.425 Fit side-chains REVERT: A 171 MET cc_start: 0.8120 (ttp) cc_final: 0.6873 (ttm) REVERT: A 521 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 547 HIS cc_start: 0.7486 (m170) cc_final: 0.6985 (m90) outliers start: 22 outliers final: 11 residues processed: 113 average time/residue: 0.1169 time to fit residues: 17.7671 Evaluate side-chains 101 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3573 r_free = 0.3573 target = 0.126179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106938 restraints weight = 8185.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109943 restraints weight = 4302.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112007 restraints weight = 2788.599| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4201 Z= 0.212 Angle : 0.690 7.746 5723 Z= 0.331 Chirality : 0.048 0.484 701 Planarity : 0.004 0.054 694 Dihedral : 14.223 91.452 693 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.72 % Allowed : 21.63 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.38), residues: 534 helix: 1.34 (0.30), residues: 328 sheet: -1.41 (1.74), residues: 10 loop : -2.77 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.002 0.001 HIS A 615 PHE 0.011 0.001 PHE A 428 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG A 340 *********************** 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 114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.471 Fit side-chains REVERT: A 262 MET cc_start: 0.8671 (mmm) cc_final: 0.8393 (mmm) REVERT: A 385 ASP cc_start: 0.8442 (t0) cc_final: 0.8083 (t0) REVERT: A 521 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 547 HIS cc_start: 0.7466 (m170) cc_final: 0.6996 (m90) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.1177 time to fit residues: 17.0188 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 : 0.472 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3561 r_free = 0.3561 target = 0.124995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105864 restraints weight = 8391.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108811 restraints weight = 4448.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110831 restraints weight = 2899.099| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4201 Z= 0.214 Angle : 0.666 7.631 5723 Z= 0.322 Chirality : 0.048 0.494 701 Planarity : 0.004 0.054 694 Dihedral : 13.106 86.871 693 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.42 % Allowed : 23.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.38), residues: 534 helix: 1.49 (0.30), residues: 327 sheet: -1.08 (1.79), residues: 10 loop : -2.69 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 635 HIS 0.000 0.000 HIS A 547 PHE 0.012 0.001 PHE A 428 TYR 0.008 0.001 TYR A 272 ARG 0.001 0.000 ARG A 603 *********************** 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 117 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 262 MET cc_start: 0.8640 (mmm) cc_final: 0.8372 (mmm) REVERT: A 520 LEU cc_start: 0.9139 (mt) cc_final: 0.8695 (mt) REVERT: A 521 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8573 (tm-30) REVERT: A 547 HIS cc_start: 0.7562 (m170) cc_final: 0.7045 (m90) REVERT: A 615 HIS cc_start: 0.7817 (t-90) cc_final: 0.7565 (t-90) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 0.1034 time to fit residues: 15.7230 Evaluate side-chains 106 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3570 r_free = 0.3570 target = 0.125652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106478 restraints weight = 8197.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109421 restraints weight = 4390.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111287 restraints weight = 2879.670| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4201 Z= 0.208 Angle : 0.672 7.485 5723 Z= 0.321 Chirality : 0.047 0.501 701 Planarity : 0.004 0.051 694 Dihedral : 12.424 83.449 693 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.19 % Allowed : 24.42 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.38), residues: 534 helix: 1.60 (0.30), residues: 327 sheet: -0.87 (1.84), residues: 10 loop : -2.62 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 PHE 0.012 0.001 PHE A 428 TYR 0.010 0.001 TYR A 614 ARG 0.002 0.000 ARG A 117 *********************** 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 120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.416 Fit side-chains REVERT: A 262 MET cc_start: 0.8587 (mmm) cc_final: 0.8327 (mmm) REVERT: A 297 LYS cc_start: 0.8405 (mptt) cc_final: 0.7821 (tmtt) REVERT: A 385 ASP cc_start: 0.8368 (t0) cc_final: 0.8079 (t0) REVERT: A 520 LEU cc_start: 0.9155 (mt) cc_final: 0.8727 (mt) REVERT: A 521 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 547 HIS cc_start: 0.7571 (m170) cc_final: 0.7052 (m90) REVERT: A 615 HIS cc_start: 0.7824 (t-90) cc_final: 0.7579 (t-90) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.1096 time to fit residues: 16.5104 Evaluate side-chains 108 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 559 LEU 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 636 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3571 r_free = 0.3571 target = 0.125883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106707 restraints weight = 8155.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109635 restraints weight = 4365.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111642 restraints weight = 2869.240| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4201 Z= 0.199 Angle : 0.672 7.328 5723 Z= 0.320 Chirality : 0.047 0.513 701 Planarity : 0.004 0.051 694 Dihedral : 11.751 80.110 693 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.65 % Allowed : 24.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.39), residues: 534 helix: 1.70 (0.30), residues: 327 sheet: -0.81 (1.84), residues: 10 loop : -2.57 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 PHE 0.011 0.001 PHE A 428 TYR 0.008 0.001 TYR A 614 ARG 0.001 0.000 ARG A 117 *********************** 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 117 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.435 Fit side-chains REVERT: A 262 MET cc_start: 0.8609 (mmm) cc_final: 0.8378 (mmm) REVERT: A 297 LYS cc_start: 0.8423 (mptt) cc_final: 0.7815 (tmtt) REVERT: A 358 GLN cc_start: 0.7415 (tt0) cc_final: 0.7104 (tt0) REVERT: A 520 LEU cc_start: 0.9158 (mt) cc_final: 0.8735 (mt) REVERT: A 521 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 547 HIS cc_start: 0.7574 (m170) cc_final: 0.7047 (m90) outliers start: 20 outliers final: 15 residues processed: 108 average time/residue: 0.1123 time to fit residues: 16.6007 Evaluate side-chains 106 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 257 CYS 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 559 LEU 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 636 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107832 restraints weight = 8064.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110822 restraints weight = 4366.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112830 restraints weight = 2865.821| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4201 Z= 0.186 Angle : 0.679 7.386 5723 Z= 0.322 Chirality : 0.048 0.546 701 Planarity : 0.004 0.050 694 Dihedral : 10.867 75.442 693 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.95 % Allowed : 25.12 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.39), residues: 534 helix: 1.82 (0.30), residues: 327 sheet: -0.78 (1.82), residues: 10 loop : -2.48 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 PHE 0.010 0.001 PHE A 428 TYR 0.008 0.001 TYR A 614 ARG 0.002 0.000 ARG A 483 *********************** 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 116 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.426 Fit side-chains REVERT: A 262 MET cc_start: 0.8571 (mmm) cc_final: 0.8351 (mmm) REVERT: A 297 LYS cc_start: 0.8427 (mptt) cc_final: 0.7788 (tmtt) REVERT: A 358 GLN cc_start: 0.7507 (tt0) cc_final: 0.7212 (tt0) REVERT: A 520 LEU cc_start: 0.9155 (mt) cc_final: 0.8718 (mt) REVERT: A 521 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 566 GLU cc_start: 0.8053 (tp30) cc_final: 0.7547 (tp30) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.1174 time to fit residues: 17.2668 Evaluate side-chains 109 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 636 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117489 restraints weight = 7741.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120597 restraints weight = 3844.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122551 restraints weight = 2413.953| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4201 Z= 0.182 Angle : 0.716 8.771 5723 Z= 0.334 Chirality : 0.048 0.544 701 Planarity : 0.004 0.051 694 Dihedral : 10.326 72.369 693 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.49 % Allowed : 26.51 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.39), residues: 534 helix: 1.81 (0.30), residues: 327 sheet: -0.70 (1.77), residues: 10 loop : -2.54 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 PHE 0.009 0.001 PHE A 428 TYR 0.006 0.001 TYR A 614 ARG 0.004 0.000 ARG A 117 *********************** 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 112 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.453 Fit side-chains REVERT: A 262 MET cc_start: 0.8549 (mmm) cc_final: 0.8337 (mmm) REVERT: A 358 GLN cc_start: 0.7484 (tt0) cc_final: 0.7174 (tt0) REVERT: A 520 LEU cc_start: 0.9149 (mt) cc_final: 0.8721 (mt) REVERT: A 521 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 566 GLU cc_start: 0.8133 (tp30) cc_final: 0.7693 (tp30) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.1081 time to fit residues: 15.7984 Evaluate side-chains 105 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 257 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3724 r_free = 0.3724 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116626 restraints weight = 7773.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119685 restraints weight = 3850.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121809 restraints weight = 2415.013| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.047 4201 Z= 0.205 Angle : 0.724 7.534 5723 Z= 0.338 Chirality : 0.050 0.577 701 Planarity : 0.004 0.052 694 Dihedral : 9.658 67.986 693 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.49 % Allowed : 26.74 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.39), residues: 534 helix: 1.77 (0.30), residues: 327 sheet: -0.67 (1.75), residues: 10 loop : -2.48 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 PHE 0.010 0.001 PHE A 428 TYR 0.007 0.001 TYR A 614 ARG 0.002 0.000 ARG A 252 ********************** 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 112 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.430 Fit side-chains REVERT: A 358 GLN cc_start: 0.7436 (tt0) cc_final: 0.7132 (tt0) REVERT: A 520 LEU cc_start: 0.9154 (mt) cc_final: 0.8722 (mt) REVERT: A 521 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 566 GLU cc_start: 0.8126 (tp30) cc_final: 0.7662 (tp30) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.1074 time to fit residues: 15.5170 Evaluate side-chains 105 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 257 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 27 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116934 restraints weight = 7778.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120017 restraints weight = 3915.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121922 restraints weight = 2453.567| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4201 Z= 0.208 Angle : 0.779 15.626 5723 Z= 0.362 Chirality : 0.050 0.584 701 Planarity : 0.004 0.052 694 Dihedral : 9.243 65.041 693 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.49 % Allowed : 27.44 % Favored : 69.07 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.38), residues: 534 helix: 1.70 (0.30), residues: 327 sheet: -0.44 (1.80), residues: 10 loop : -2.43 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.000 0.000 HIS A 615 PHE 0.011 0.001 PHE A 428 TYR 0.010 0.001 TYR A 272 ARG 0.002 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.84 seconds wall clock time: 28 minutes 1.14 seconds (1681.14 seconds total)