Starting phenix.real_space_refine on Thu Jul 2 02:56:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2026/7zdq_14666.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4010 2.51 5 N 1037 2.21 5 O 1184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6264 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "B" Number of atoms: 1345 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1339 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 166, 1339 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain breaks: 2 bond proxies already assigned to first conformer: 1370 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.36, per 1000 atoms: 0.38 Number of scatterers: 6264 At special positions: 0 Unit cell: (96.025, 98.53, 91.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1184 8.00 N 1037 7.00 C 4010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 53 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 595.0 milliseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 58.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.543A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.827A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.566A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.538A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.608A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.986A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.692A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.687A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.584A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.401A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.538A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.063A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.268A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.948A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.521A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 907 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: 0.96 Time building geometry restraints manager: 0.71 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: 2010 1.35 - 1.47: 1677 1.47 - 1.59: 2701 1.59 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6442 Sorted by residual: bond pdb=" C GLU A 589 " pdb=" N PRO A 590 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.31e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8459 1.34 - 2.67: 224 2.67 - 4.01: 50 4.01 - 5.34: 16 5.34 - 6.68: 3 Bond angle restraints: 8752 Sorted by residual: angle pdb=" N LEU A 39 " pdb=" CA LEU A 39 " pdb=" C LEU A 39 " ideal model delta sigma weight residual 113.41 108.45 4.96 1.22e+00 6.72e-01 1.65e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 113.20 109.47 3.73 9.60e-01 1.09e+00 1.51e+01 angle pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta sigma weight residual 120.82 124.88 -4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" CA ALA A 614 " pdb=" C ALA A 614 " pdb=" N ASP A 615 " ideal model delta sigma weight residual 119.26 116.40 2.86 1.14e+00 7.69e-01 6.31e+00 angle pdb=" C ALA A 614 " pdb=" N ASP A 615 " pdb=" CA ASP A 615 " ideal model delta sigma weight residual 121.70 126.14 -4.44 1.80e+00 3.09e-01 6.09e+00 ... (remaining 8747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3373 18.00 - 36.00: 311 36.00 - 54.00: 55 54.00 - 71.99: 18 71.99 - 89.99: 11 Dihedral angle restraints: 3768 sinusoidal: 1524 harmonic: 2244 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 25.70 67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -122.22 36.22 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 644 0.035 - 0.070: 184 0.070 - 0.105: 73 0.105 - 0.140: 14 0.140 - 0.175: 1 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA TYR A 385 " pdb=" N TYR A 385 " pdb=" C TYR A 385 " pdb=" CB TYR A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 913 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.55e+00 pdb=" N PRO A 346 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 171 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CD GLU A 171 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 171 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 171 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 500 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.022 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 655 2.75 - 3.29: 6118 3.29 - 3.82: 10709 3.82 - 4.36: 12709 4.36 - 4.90: 21987 Nonbonded interactions: 52178 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 425 " pdb=" OD1 ASP A 427 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 229 " pdb=" OH TYR A 516 " model vdw 2.249 3.040 nonbonded pdb=" O ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.277 3.040 ... (remaining 52173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.003 0.045 6450 Z= 0.134 Angle : 0.557 6.676 8771 Z= 0.315 Chirality : 0.040 0.175 916 Planarity : 0.004 0.077 1132 Dihedral : 15.222 89.992 2315 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.48 (0.31), residues: 757 helix: 2.02 (0.27), residues: 394 sheet: 1.39 (0.85), residues: 39 loop : -0.37 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.008 0.001 TYR A 381 PHE 0.021 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 6442) covalent geometry : angle 0.55528 / 0.31 ( 8752) SS BOND : bond 0.00327 / 0.17 ( 5) SS BOND : angle 1.25207 / 0.68 ( 10) hydrogen bonds : bond 0.11812 / 7.51 ( 317) hydrogen bonds : angle 5.52982 / 3.89 ( 907) link_NAG-ASN : bond 0.00195 / 0.09 ( 3) link_NAG-ASN : angle 1.14455 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.172 Fit side-chains REVERT: A 483 GLU cc_start: 0.7025 (mp0) cc_final: 0.6688 (mp0) REVERT: A 568 LEU cc_start: 0.7999 (tt) cc_final: 0.7580 (mp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0933 time to fit residues: 10.9653 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN B 498 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.137583 restraints weight = 10894.846| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.00 r_work: 0.3261 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6450 Z= 0.107 Angle : 0.486 5.961 8771 Z= 0.254 Chirality : 0.040 0.161 916 Planarity : 0.004 0.054 1132 Dihedral : 3.768 19.276 833 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.74 % Allowed : 4.02 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.55 (0.31), residues: 757 helix: 2.07 (0.26), residues: 392 sheet: 1.10 (0.84), residues: 40 loop : -0.26 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.026 0.001 TYR A 385 PHE 0.019 0.001 PHE A 369 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6442) covalent geometry : angle 0.48377 / 0.25 ( 8752) SS BOND : bond 0.00438 / 0.22 ( 5) SS BOND : angle 1.10335 / 0.59 ( 10) hydrogen bonds : bond 0.04438 / 2.92 ( 317) hydrogen bonds : angle 4.51996 / 3.15 ( 907) link_NAG-ASN : bond 0.00244 / 0.12 ( 3) link_NAG-ASN : angle 1.21058 / 0.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.231 Fit side-chains REVERT: A 34 HIS cc_start: 0.8145 (m90) cc_final: 0.7938 (m90) REVERT: A 492 PRO cc_start: 0.7742 (Cg_exo) cc_final: 0.7488 (Cg_endo) REVERT: B 449 TYR cc_start: 0.7878 (m-80) cc_final: 0.7633 (m-80) outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 0.0810 time to fit residues: 9.6238 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 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 = 0.3630 r_free = 0.3630 target = 0.152196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.124837 restraints weight = 16456.917| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.80 r_work: 0.2997 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6450 Z= 0.193 Angle : 0.579 5.981 8771 Z= 0.303 Chirality : 0.044 0.146 916 Planarity : 0.004 0.044 1132 Dihedral : 4.243 22.531 833 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.34 % Allowed : 5.21 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.08 (0.31), residues: 757 helix: 1.61 (0.26), residues: 399 sheet: 0.48 (0.75), residues: 51 loop : -0.37 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 457 TYR 0.030 0.002 TYR A 385 PHE 0.023 0.002 PHE A 400 TRP 0.012 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 6442) covalent geometry : angle 0.57387 / 0.30 ( 8752) SS BOND : bond 0.00603 / 0.30 ( 5) SS BOND : angle 1.54136 / 0.82 ( 10) hydrogen bonds : bond 0.06156 / 4.03 ( 317) hydrogen bonds : angle 4.70786 / 3.31 ( 907) link_NAG-ASN : bond 0.00234 / 0.12 ( 3) link_NAG-ASN : angle 1.83116 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.180 Fit side-chains REVERT: A 171 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: A 492 PRO cc_start: 0.7764 (Cg_exo) cc_final: 0.7466 (Cg_endo) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 0.0774 time to fit residues: 8.3209 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.161303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135243 restraints weight = 11794.097| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.83 r_work: 0.3227 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6450 Z= 0.108 Angle : 0.484 5.896 8771 Z= 0.251 Chirality : 0.039 0.130 916 Planarity : 0.004 0.041 1132 Dihedral : 3.914 20.013 833 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.74 % Allowed : 5.80 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.32 (0.31), residues: 757 helix: 1.83 (0.26), residues: 400 sheet: 0.32 (0.75), residues: 51 loop : -0.27 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.024 0.001 TYR A 385 PHE 0.019 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 6442) covalent geometry : angle 0.48087 / 0.25 ( 8752) SS BOND : bond 0.00378 / 0.19 ( 5) SS BOND : angle 1.05006 / 0.56 ( 10) hydrogen bonds : bond 0.04538 / 3.00 ( 317) hydrogen bonds : angle 4.45307 / 3.12 ( 907) link_NAG-ASN : bond 0.00231 / 0.11 ( 3) link_NAG-ASN : angle 1.39914 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.158 Fit side-chains REVERT: A 492 PRO cc_start: 0.7694 (Cg_exo) cc_final: 0.7421 (Cg_endo) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.0711 time to fit residues: 7.9325 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 72 optimal weight: 0.0470 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.162199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134864 restraints weight = 14197.610| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.58 r_work: 0.3207 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6450 Z= 0.108 Angle : 0.479 5.839 8771 Z= 0.250 Chirality : 0.040 0.124 916 Planarity : 0.003 0.038 1132 Dihedral : 3.829 21.064 833 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.60 % Allowed : 7.29 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.43 (0.31), residues: 757 helix: 1.94 (0.26), residues: 400 sheet: 0.25 (0.75), residues: 51 loop : -0.21 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.023 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 6442) covalent geometry : angle 0.47602 / 0.25 ( 8752) SS BOND : bond 0.00371 / 0.19 ( 5) SS BOND : angle 0.98905 / 0.53 ( 10) hydrogen bonds : bond 0.04482 / 2.96 ( 317) hydrogen bonds : angle 4.39211 / 3.07 ( 907) link_NAG-ASN : bond 0.00211 / 0.10 ( 3) link_NAG-ASN : angle 1.40130 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.185 Fit side-chains REVERT: A 492 PRO cc_start: 0.7737 (Cg_exo) cc_final: 0.7488 (Cg_endo) REVERT: A 548 THR cc_start: 0.8008 (m) cc_final: 0.7408 (p) outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.0747 time to fit residues: 7.9058 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.0000 chunk 48 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 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 = 0.3717 r_free = 0.3717 target = 0.159194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.131948 restraints weight = 18111.390| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.71 r_work: 0.3047 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6450 Z= 0.133 Angle : 0.506 5.903 8771 Z= 0.265 Chirality : 0.041 0.132 916 Planarity : 0.004 0.036 1132 Dihedral : 3.946 20.648 833 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.34 % Allowed : 6.85 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.34 (0.31), residues: 757 helix: 1.85 (0.26), residues: 400 sheet: 0.24 (0.74), residues: 51 loop : -0.25 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.024 0.001 TYR A 385 PHE 0.019 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6442) covalent geometry : angle 0.50289 / 0.26 ( 8752) SS BOND : bond 0.00440 / 0.22 ( 5) SS BOND : angle 1.13737 / 0.61 ( 10) hydrogen bonds : bond 0.05106 / 3.36 ( 317) hydrogen bonds : angle 4.46518 / 3.14 ( 907) link_NAG-ASN : bond 0.00194 / 0.10 ( 3) link_NAG-ASN : angle 1.54577 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.234 Fit side-chains REVERT: A 492 PRO cc_start: 0.7758 (Cg_exo) cc_final: 0.7489 (Cg_endo) REVERT: A 548 THR cc_start: 0.8046 (m) cc_final: 0.7419 (p) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.0760 time to fit residues: 8.4863 Evaluate side-chains 81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.164564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.138688 restraints weight = 12123.067| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.99 r_work: 0.3248 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6450 Z= 0.096 Angle : 0.457 5.855 8771 Z= 0.238 Chirality : 0.039 0.119 916 Planarity : 0.003 0.035 1132 Dihedral : 3.717 20.605 833 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.89 % Allowed : 7.29 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.60 (0.32), residues: 757 helix: 2.08 (0.26), residues: 400 sheet: 0.21 (0.74), residues: 51 loop : -0.12 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.020 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 ( 6442) covalent geometry : angle 0.45513 / 0.24 ( 8752) SS BOND : bond 0.00307 / 0.16 ( 5) SS BOND : angle 0.87967 / 0.47 ( 10) hydrogen bonds : bond 0.04017 / 2.67 ( 317) hydrogen bonds : angle 4.31279 / 3.01 ( 907) link_NAG-ASN : bond 0.00229 / 0.11 ( 3) link_NAG-ASN : angle 1.27508 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.183 Fit side-chains REVERT: A 492 PRO cc_start: 0.7724 (Cg_exo) cc_final: 0.7467 (Cg_endo) REVERT: A 548 THR cc_start: 0.7975 (m) cc_final: 0.7371 (p) REVERT: B 420 ASP cc_start: 0.7883 (m-30) cc_final: 0.7378 (m-30) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.0700 time to fit residues: 7.4524 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 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 = 0.3648 r_free = 0.3648 target = 0.154041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.127184 restraints weight = 13276.448| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.59 r_work: 0.3102 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6450 Z= 0.170 Angle : 0.555 6.430 8771 Z= 0.288 Chirality : 0.042 0.145 916 Planarity : 0.004 0.033 1132 Dihedral : 4.096 21.283 833 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 7.44 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.26 (0.31), residues: 757 helix: 1.77 (0.26), residues: 401 sheet: 0.27 (0.75), residues: 51 loop : -0.26 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.027 0.002 TYR A 385 PHE 0.019 0.002 PHE A 400 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6442) covalent geometry : angle 0.55105 / 0.29 ( 8752) SS BOND : bond 0.00508 / 0.26 ( 5) SS BOND : angle 1.28535 / 0.69 ( 10) hydrogen bonds : bond 0.05688 / 3.72 ( 317) hydrogen bonds : angle 4.52812 / 3.18 ( 907) link_NAG-ASN : bond 0.00159 / 0.08 ( 3) link_NAG-ASN : angle 1.62961 / 0.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.233 Fit side-chains REVERT: A 492 PRO cc_start: 0.7751 (Cg_exo) cc_final: 0.7496 (Cg_endo) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.0802 time to fit residues: 8.4921 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 403 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.0020 chunk 58 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134560 restraints weight = 17110.834| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.41 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6450 Z= 0.108 Angle : 0.486 5.877 8771 Z= 0.252 Chirality : 0.039 0.121 916 Planarity : 0.003 0.034 1132 Dihedral : 3.879 21.080 833 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.74 % Allowed : 7.74 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.47 (0.31), residues: 757 helix: 1.94 (0.26), residues: 401 sheet: 0.21 (0.75), residues: 51 loop : -0.15 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.021 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6442) covalent geometry : angle 0.48300 / 0.25 ( 8752) SS BOND : bond 0.00364 / 0.19 ( 5) SS BOND : angle 0.98128 / 0.53 ( 10) hydrogen bonds : bond 0.04509 / 2.98 ( 317) hydrogen bonds : angle 4.38451 / 3.06 ( 907) link_NAG-ASN : bond 0.00220 / 0.11 ( 3) link_NAG-ASN : angle 1.38633 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.139 Fit side-chains REVERT: A 376 MET cc_start: 0.7988 (tpp) cc_final: 0.7656 (tpp) REVERT: A 492 PRO cc_start: 0.7583 (Cg_exo) cc_final: 0.7358 (Cg_endo) REVERT: A 548 THR cc_start: 0.7889 (m) cc_final: 0.7293 (p) outliers start: 4 outliers final: 4 residues processed: 78 average time/residue: 0.0745 time to fit residues: 7.8236 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.162481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135102 restraints weight = 10261.683| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.99 r_work: 0.3232 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6450 Z= 0.106 Angle : 0.482 5.865 8771 Z= 0.250 Chirality : 0.039 0.121 916 Planarity : 0.003 0.033 1132 Dihedral : 3.782 20.264 833 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.74 % Allowed : 7.74 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.53 (0.31), residues: 757 helix: 2.02 (0.26), residues: 400 sheet: 0.17 (0.74), residues: 51 loop : -0.15 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.021 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6442) covalent geometry : angle 0.47935 / 0.25 ( 8752) SS BOND : bond 0.00342 / 0.18 ( 5) SS BOND : angle 0.98280 / 0.53 ( 10) hydrogen bonds : bond 0.04423 / 2.92 ( 317) hydrogen bonds : angle 4.34226 / 3.02 ( 907) link_NAG-ASN : bond 0.00214 / 0.10 ( 3) link_NAG-ASN : angle 1.35184 / 0.73 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.273 Fit side-chains REVERT: A 492 PRO cc_start: 0.7737 (Cg_exo) cc_final: 0.7513 (Cg_endo) REVERT: A 548 THR cc_start: 0.8001 (m) cc_final: 0.7399 (p) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 0.0804 time to fit residues: 8.3156 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.137247 restraints weight = 17088.464| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.30 r_work: 0.3129 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6450 Z= 0.101 Angle : 0.473 5.843 8771 Z= 0.245 Chirality : 0.039 0.120 916 Planarity : 0.003 0.033 1132 Dihedral : 3.729 20.375 833 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 7.44 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.61 (0.32), residues: 757 helix: 2.08 (0.26), residues: 400 sheet: 0.21 (0.74), residues: 51 loop : -0.11 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 457 TYR 0.021 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6442) covalent geometry : angle 0.47081 / 0.24 ( 8752) SS BOND : bond 0.00324 / 0.17 ( 5) SS BOND : angle 0.92063 / 0.50 ( 10) hydrogen bonds : bond 0.04173 / 2.76 ( 317) hydrogen bonds : angle 4.30439 / 3.00 ( 907) link_NAG-ASN : bond 0.00219 / 0.11 ( 3) link_NAG-ASN : angle 1.28814 / 0.70 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.20 seconds wall clock time: 27 minutes 21.04 seconds (1641.04 seconds total)