Starting phenix.real_space_refine on Wed Sep 17 06:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.map" model { file = "/net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iup_60911/09_2025/9iup_60911.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.086 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 37 5.16 5 C 4115 2.51 5 N 1064 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6420 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1547 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.85, per 1000 atoms: 0.29 Number of scatterers: 6420 At special positions: 0 Unit cell: (73.528, 81.608, 118.776, 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 37 16.00 O 1204 8.00 N 1064 7.00 C 4115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 B 601 " - " ASN B 343 " " NAG B 602 " - " ASN B 354 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 454.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 56.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.531A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.995A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.895A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.621A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (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 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.520A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.907A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.823A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.558A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.820A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.508A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.580A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.803A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.967A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.729A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.130A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.502A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.749A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.561A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 314 hydrogen bonds defined for protein. 888 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: 0.92 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1066 1.31 - 1.44: 1927 1.44 - 1.58: 3556 1.58 - 1.72: 0 1.72 - 1.86: 58 Bond restraints: 6607 Sorted by residual: bond pdb=" C PHE A 32 " pdb=" O PHE A 32 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.16e-02 7.43e+03 3.52e+01 bond pdb=" CA ALA A 36 " pdb=" CB ALA A 36 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.59e-02 3.96e+03 3.21e+01 bond pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 1.526 1.457 0.069 1.22e-02 6.72e+03 3.20e+01 bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.529 1.441 0.089 1.58e-02 4.01e+03 3.14e+01 bond pdb=" CA TYR A 41 " pdb=" C TYR A 41 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.35e-02 5.49e+03 3.11e+01 ... (remaining 6602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 8906 3.41 - 6.81: 65 6.81 - 10.22: 6 10.22 - 13.63: 2 13.63 - 17.04: 1 Bond angle restraints: 8980 Sorted by residual: angle pdb=" C TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta sigma weight residual 110.67 93.63 17.04 1.92e+00 2.71e-01 7.87e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 127.41 -13.51 1.80e+00 3.09e-01 5.64e+01 angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 127.64 -13.24 2.30e+00 1.89e-01 3.31e+01 angle pdb=" C HIS A 34 " pdb=" CA HIS A 34 " pdb=" CB HIS A 34 " ideal model delta sigma weight residual 110.96 102.19 8.77 1.54e+00 4.22e-01 3.24e+01 angle pdb=" C ASN A 33 " pdb=" CA ASN A 33 " pdb=" CB ASN A 33 " ideal model delta sigma weight residual 110.84 120.26 -9.42 1.66e+00 3.63e-01 3.22e+01 ... (remaining 8975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 3282 15.94 - 31.88: 455 31.88 - 47.81: 145 47.81 - 63.75: 31 63.75 - 79.69: 13 Dihedral angle restraints: 3926 sinusoidal: 1615 harmonic: 2311 Sorted by residual: dihedral pdb=" C TYR A 41 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta harmonic sigma weight residual -122.60 -102.81 -19.79 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.69 64.31 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 155.72 -62.72 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 3923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 812 0.062 - 0.124: 116 0.124 - 0.186: 6 0.186 - 0.248: 2 0.248 - 0.310: 3 Chirality restraints: 939 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA GLU B 493 " pdb=" N GLU B 493 " pdb=" C GLU B 493 " pdb=" CB GLU B 493 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASN A 33 " pdb=" N ASN A 33 " pdb=" C ASN A 33 " pdb=" CB ASN A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 936 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 495 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C TYR B 495 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B 495 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 496 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 493 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C GLU B 493 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU B 493 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 494 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 37 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLU A 37 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 37 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 38 " 0.014 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 139 2.69 - 3.24: 6180 3.24 - 3.79: 10243 3.79 - 4.35: 13276 4.35 - 4.90: 22740 Nonbonded interactions: 52578 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OD2 ASP A 355 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.280 3.040 ... (remaining 52573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.090 6616 Z= 0.314 Angle : 0.740 17.037 9000 Z= 0.449 Chirality : 0.046 0.310 939 Planarity : 0.004 0.037 1161 Dihedral : 16.868 79.689 2421 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.14 % Allowed : 19.08 % Favored : 80.78 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.31), residues: 783 helix: 1.40 (0.27), residues: 393 sheet: -1.37 (0.89), residues: 45 loop : -0.57 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.038 0.002 TYR B 495 PHE 0.019 0.001 PHE A 40 TRP 0.010 0.001 TRP A 594 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 6607) covalent geometry : angle 0.73285 ( 8980) SS BOND : bond 0.00672 ( 7) SS BOND : angle 1.93483 ( 14) hydrogen bonds : bond 0.15698 ( 308) hydrogen bonds : angle 6.12297 ( 888) link_NAG-ASN : bond 0.00832 ( 2) link_NAG-ASN : angle 3.07390 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (mmtt) REVERT: A 325 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7106 (tp-100) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0919 time to fit residues: 10.3043 Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.174206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135564 restraints weight = 7304.983| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.52 r_work: 0.3094 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6616 Z= 0.138 Angle : 0.533 7.627 9000 Z= 0.274 Chirality : 0.041 0.240 939 Planarity : 0.004 0.037 1161 Dihedral : 4.342 56.446 899 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.59 % Allowed : 16.62 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.31), residues: 783 helix: 1.30 (0.26), residues: 406 sheet: -1.48 (0.87), residues: 44 loop : -0.61 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.019 0.002 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6607) covalent geometry : angle 0.52907 ( 8980) SS BOND : bond 0.00440 ( 7) SS BOND : angle 1.06692 ( 14) hydrogen bonds : bond 0.04622 ( 308) hydrogen bonds : angle 4.29110 ( 888) link_NAG-ASN : bond 0.00726 ( 2) link_NAG-ASN : angle 2.29364 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7905 (mmtt) REVERT: A 325 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7015 (tp-100) REVERT: A 465 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7316 (ttmm) REVERT: A 482 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8062 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.0837 time to fit residues: 10.3503 Evaluate side-chains 84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.189492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.154235 restraints weight = 7120.881| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.88 r_work: 0.3179 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6616 Z= 0.114 Angle : 0.495 6.385 9000 Z= 0.254 Chirality : 0.040 0.209 939 Planarity : 0.003 0.036 1161 Dihedral : 4.136 55.507 899 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 16.33 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.31), residues: 783 helix: 1.36 (0.26), residues: 408 sheet: -1.66 (0.77), residues: 54 loop : -0.54 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6607) covalent geometry : angle 0.49277 ( 8980) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.89308 ( 14) hydrogen bonds : bond 0.04138 ( 308) hydrogen bonds : angle 4.04698 ( 888) link_NAG-ASN : bond 0.00461 ( 2) link_NAG-ASN : angle 1.62388 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8169 (mmtt) REVERT: A 366 MET cc_start: 0.8076 (tpt) cc_final: 0.7525 (tpp) REVERT: A 465 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7425 (ttmm) REVERT: A 482 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: A 489 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: B 394 ASN cc_start: 0.7754 (m-40) cc_final: 0.7512 (m-40) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.0752 time to fit residues: 9.7650 Evaluate side-chains 88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.173676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135071 restraints weight = 7262.265| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.49 r_work: 0.3097 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6616 Z= 0.130 Angle : 0.508 6.596 9000 Z= 0.258 Chirality : 0.040 0.198 939 Planarity : 0.003 0.036 1161 Dihedral : 4.122 55.099 899 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.46 % Allowed : 17.34 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.31), residues: 783 helix: 1.36 (0.26), residues: 407 sheet: -1.46 (0.78), residues: 54 loop : -0.52 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6607) covalent geometry : angle 0.50558 ( 8980) SS BOND : bond 0.00437 ( 7) SS BOND : angle 0.97361 ( 14) hydrogen bonds : bond 0.04170 ( 308) hydrogen bonds : angle 3.97106 ( 888) link_NAG-ASN : bond 0.00430 ( 2) link_NAG-ASN : angle 1.41558 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (mmtt) REVERT: A 189 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 366 MET cc_start: 0.8004 (tpt) cc_final: 0.7451 (tpp) REVERT: A 465 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7423 (ttmm) REVERT: A 474 MET cc_start: 0.7818 (mmp) cc_final: 0.7603 (mmp) REVERT: A 482 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8138 (mmm-85) REVERT: A 489 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: B 394 ASN cc_start: 0.7617 (m-40) cc_final: 0.7332 (m-40) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.0792 time to fit residues: 9.7803 Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 20.0000 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.173805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134168 restraints weight = 7310.391| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.58 r_work: 0.3096 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6616 Z= 0.120 Angle : 0.499 6.740 9000 Z= 0.254 Chirality : 0.040 0.185 939 Planarity : 0.003 0.036 1161 Dihedral : 4.075 54.652 899 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 17.49 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.31), residues: 783 helix: 1.42 (0.26), residues: 407 sheet: -1.32 (0.76), residues: 54 loop : -0.47 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6607) covalent geometry : angle 0.49685 ( 8980) SS BOND : bond 0.00563 ( 7) SS BOND : angle 0.87067 ( 14) hydrogen bonds : bond 0.04049 ( 308) hydrogen bonds : angle 3.87240 ( 888) link_NAG-ASN : bond 0.00383 ( 2) link_NAG-ASN : angle 1.26970 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8068 (mmtt) REVERT: A 145 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 189 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 366 MET cc_start: 0.8046 (tpt) cc_final: 0.7498 (tpp) REVERT: A 465 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7423 (ttmm) REVERT: A 482 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: A 489 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: B 394 ASN cc_start: 0.7546 (m-40) cc_final: 0.7321 (m-40) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.0775 time to fit residues: 10.2875 Evaluate side-chains 90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 445 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.195476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156201 restraints weight = 7428.190| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.33 r_work: 0.3320 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6616 Z= 0.203 Angle : 0.584 7.927 9000 Z= 0.296 Chirality : 0.043 0.184 939 Planarity : 0.004 0.036 1161 Dihedral : 4.410 54.845 899 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.18 % Allowed : 17.20 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.30), residues: 783 helix: 1.23 (0.26), residues: 402 sheet: -1.28 (0.74), residues: 54 loop : -0.54 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.021 0.002 TYR A 385 PHE 0.015 0.001 PHE A 523 TRP 0.010 0.001 TRP A 271 HIS 0.007 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 6607) covalent geometry : angle 0.58204 ( 8980) SS BOND : bond 0.00582 ( 7) SS BOND : angle 1.07470 ( 14) hydrogen bonds : bond 0.04799 ( 308) hydrogen bonds : angle 4.03576 ( 888) link_NAG-ASN : bond 0.00531 ( 2) link_NAG-ASN : angle 1.44606 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8284 (mmtt) REVERT: A 145 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 154 ASN cc_start: 0.8842 (p0) cc_final: 0.8489 (p0) REVERT: A 189 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 216 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7680 (p0) REVERT: A 465 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7465 (ttmm) REVERT: A 489 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 394 ASN cc_start: 0.7718 (m-40) cc_final: 0.7466 (m-40) outliers start: 22 outliers final: 15 residues processed: 98 average time/residue: 0.0725 time to fit residues: 10.0021 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.197755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156462 restraints weight = 7361.834| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.53 r_work: 0.3372 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6616 Z= 0.147 Angle : 0.538 8.399 9000 Z= 0.272 Chirality : 0.041 0.182 939 Planarity : 0.004 0.037 1161 Dihedral : 4.287 53.945 899 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.18 % Allowed : 18.64 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.30), residues: 783 helix: 1.16 (0.26), residues: 407 sheet: -1.15 (0.74), residues: 54 loop : -0.49 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.009 0.001 TRP B 353 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6607) covalent geometry : angle 0.53588 ( 8980) SS BOND : bond 0.00575 ( 7) SS BOND : angle 1.02982 ( 14) hydrogen bonds : bond 0.04365 ( 308) hydrogen bonds : angle 3.94659 ( 888) link_NAG-ASN : bond 0.00391 ( 2) link_NAG-ASN : angle 1.32657 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8213 (mmtt) REVERT: A 145 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 154 ASN cc_start: 0.8808 (p0) cc_final: 0.8463 (p0) REVERT: A 189 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 482 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: A 489 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: B 394 ASN cc_start: 0.7693 (m-40) cc_final: 0.7454 (m-40) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.0774 time to fit residues: 10.3131 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.0020 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.199776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159734 restraints weight = 7419.351| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.27 r_work: 0.3406 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6616 Z= 0.117 Angle : 0.527 8.803 9000 Z= 0.266 Chirality : 0.040 0.177 939 Planarity : 0.003 0.037 1161 Dihedral : 4.182 53.467 899 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.75 % Allowed : 18.35 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.30), residues: 783 helix: 1.17 (0.26), residues: 407 sheet: -0.93 (0.76), residues: 54 loop : -0.42 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.017 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.010 0.001 TRP B 353 HIS 0.002 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6607) covalent geometry : angle 0.52577 ( 8980) SS BOND : bond 0.00493 ( 7) SS BOND : angle 0.95917 ( 14) hydrogen bonds : bond 0.04087 ( 308) hydrogen bonds : angle 3.90379 ( 888) link_NAG-ASN : bond 0.00326 ( 2) link_NAG-ASN : angle 1.19694 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8150 (mmtt) REVERT: A 145 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 154 ASN cc_start: 0.8769 (p0) cc_final: 0.8405 (p0) REVERT: A 189 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 465 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7500 (ttmm) REVERT: A 489 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 394 ASN cc_start: 0.7726 (m-40) cc_final: 0.7463 (m-40) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0739 time to fit residues: 9.8610 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 74 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.173462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134093 restraints weight = 7409.734| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.59 r_work: 0.3091 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6616 Z= 0.115 Angle : 0.515 8.326 9000 Z= 0.262 Chirality : 0.041 0.205 939 Planarity : 0.003 0.037 1161 Dihedral : 4.141 53.256 899 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.60 % Allowed : 18.93 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 783 helix: 1.18 (0.26), residues: 407 sheet: -0.84 (0.76), residues: 54 loop : -0.37 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.026 0.001 TYR A 279 PHE 0.012 0.001 PHE A 523 TRP 0.009 0.001 TRP B 353 HIS 0.009 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6607) covalent geometry : angle 0.51363 ( 8980) SS BOND : bond 0.00463 ( 7) SS BOND : angle 0.88118 ( 14) hydrogen bonds : bond 0.04037 ( 308) hydrogen bonds : angle 3.90958 ( 888) link_NAG-ASN : bond 0.00328 ( 2) link_NAG-ASN : angle 1.14956 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 154 ASN cc_start: 0.8746 (p0) cc_final: 0.8379 (p0) REVERT: A 189 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 465 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7428 (ttmm) REVERT: A 489 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: B 394 ASN cc_start: 0.7599 (m-40) cc_final: 0.7325 (m-40) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.0702 time to fit residues: 8.9285 Evaluate side-chains 90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135092 restraints weight = 7238.169| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.43 r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6616 Z= 0.120 Angle : 0.527 8.495 9000 Z= 0.268 Chirality : 0.041 0.208 939 Planarity : 0.003 0.037 1161 Dihedral : 3.763 18.002 895 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 18.93 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 783 helix: 1.18 (0.26), residues: 410 sheet: -0.86 (0.76), residues: 54 loop : -0.40 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.019 0.001 TYR A 50 PHE 0.013 0.001 PHE A 523 TRP 0.012 0.001 TRP A 478 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6607) covalent geometry : angle 0.52519 ( 8980) SS BOND : bond 0.00461 ( 7) SS BOND : angle 0.88455 ( 14) hydrogen bonds : bond 0.04046 ( 308) hydrogen bonds : angle 3.90000 ( 888) link_NAG-ASN : bond 0.00329 ( 2) link_NAG-ASN : angle 1.13456 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 154 ASN cc_start: 0.8717 (p0) cc_final: 0.8353 (p0) REVERT: A 189 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 465 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7433 (ttmm) REVERT: A 474 MET cc_start: 0.7625 (mmp) cc_final: 0.7387 (mmp) REVERT: A 489 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: B 394 ASN cc_start: 0.7580 (m-40) cc_final: 0.7285 (m-40) outliers start: 19 outliers final: 17 residues processed: 88 average time/residue: 0.0721 time to fit residues: 8.9660 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156005 restraints weight = 7315.649| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.32 r_work: 0.3350 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6616 Z= 0.185 Angle : 0.579 8.348 9000 Z= 0.295 Chirality : 0.043 0.195 939 Planarity : 0.004 0.036 1161 Dihedral : 3.991 20.064 895 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.60 % Allowed : 19.36 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.30), residues: 783 helix: 1.11 (0.26), residues: 402 sheet: -1.00 (0.75), residues: 54 loop : -0.44 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.018 0.002 TYR A 385 PHE 0.014 0.001 PHE A 523 TRP 0.011 0.001 TRP A 271 HIS 0.010 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6607) covalent geometry : angle 0.57669 ( 8980) SS BOND : bond 0.00539 ( 7) SS BOND : angle 1.10087 ( 14) hydrogen bonds : bond 0.04584 ( 308) hydrogen bonds : angle 4.02903 ( 888) link_NAG-ASN : bond 0.00464 ( 2) link_NAG-ASN : angle 1.33059 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.06 seconds wall clock time: 28 minutes 29.54 seconds (1709.54 seconds total)