Starting phenix.real_space_refine on Thu Jun 5 21:30:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy4_25516/06_2025/7sy4_25516.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 4192 2.51 5 N 1078 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6554 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.08, per 1000 atoms: 0.78 Number of scatterers: 6554 At special positions: 0 Unit cell: (82, 84, 123, 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 1247 8.00 N 1078 7.00 C 4192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 911.2 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.754A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.006A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.516A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.775A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.056A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.944A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.726A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.658A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.768A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.610A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.709A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.279A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.558A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.375A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.719A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.509A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.917A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.945A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.753A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.050A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.333A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2079 1.35 - 1.47: 1776 1.47 - 1.59: 2824 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8787 1.96 - 3.93: 314 3.93 - 5.89: 42 5.89 - 7.85: 8 7.85 - 9.82: 4 Bond angle restraints: 9155 Sorted by residual: angle pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" C PHE E 32 " ideal model delta sigma weight residual 111.04 103.72 7.32 1.55e+00 4.16e-01 2.23e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.97 -6.15 1.42e+00 4.96e-01 1.88e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.24 -8.84 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 120.23 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 118.06 -4.90 1.42e+00 4.96e-01 1.19e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3689 17.13 - 34.26: 312 34.26 - 51.39: 45 51.39 - 68.52: 9 68.52 - 85.65: 12 Dihedral angle restraints: 4067 sinusoidal: 1728 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -43.96 -42.04 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 14.88 64.12 1 2.00e+01 2.50e-03 1.35e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 714 0.052 - 0.105: 197 0.105 - 0.157: 55 0.157 - 0.210: 10 0.210 - 0.262: 2 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 103 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 975 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ARG E 169 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG E 169 " -0.021 2.00e-02 2.50e+03 pdb=" N SER E 170 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 29 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.46e+00 pdb=" C LEU E 29 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU E 29 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP E 30 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C ALA E 36 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2205 2.86 - 3.37: 5969 3.37 - 3.88: 11213 3.88 - 4.39: 12524 4.39 - 4.90: 21658 Nonbonded interactions: 53569 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.345 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.352 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.364 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.369 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.369 3.120 ... (remaining 53564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.055 6750 Z= 0.228 Angle : 0.880 12.114 9188 Z= 0.469 Chirality : 0.055 0.262 978 Planarity : 0.007 0.063 1176 Dihedral : 13.360 85.655 2549 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 793 helix: -0.29 (0.23), residues: 387 sheet: 0.99 (0.73), residues: 43 loop : -0.68 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 165 HIS 0.005 0.001 HIS E 378 PHE 0.030 0.002 PHE E 369 TYR 0.028 0.002 TYR B 495 ARG 0.009 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 7) link_NAG-ASN : angle 4.81526 ( 21) hydrogen bonds : bond 0.13994 ( 319) hydrogen bonds : angle 6.06874 ( 906) SS BOND : bond 0.00517 ( 6) SS BOND : angle 2.62702 ( 12) covalent geometry : bond 0.00480 ( 6737) covalent geometry : angle 0.84592 ( 9155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 414 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9059 (mm-40) REVERT: B 420 ASP cc_start: 0.9060 (m-30) cc_final: 0.8777 (m-30) REVERT: E 37 GLU cc_start: 0.8226 (tt0) cc_final: 0.7840 (tp30) REVERT: E 82 MET cc_start: 0.8690 (mtp) cc_final: 0.8253 (ttm) REVERT: E 323 MET cc_start: 0.9194 (mmp) cc_final: 0.8739 (mmm) REVERT: E 367 ASP cc_start: 0.9374 (m-30) cc_final: 0.9118 (p0) REVERT: E 368 ASP cc_start: 0.8701 (m-30) cc_final: 0.8012 (m-30) REVERT: E 409 SER cc_start: 0.9539 (t) cc_final: 0.9192 (p) REVERT: E 429 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8156 (tm-30) REVERT: E 435 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8766 (mm-30) REVERT: E 462 MET cc_start: 0.9332 (mtp) cc_final: 0.9099 (mtt) REVERT: E 471 ASP cc_start: 0.8880 (p0) cc_final: 0.8604 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2481 time to fit residues: 33.5247 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.062425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046527 restraints weight = 22275.282| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.87 r_work: 0.2580 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6750 Z= 0.188 Angle : 0.599 6.794 9188 Z= 0.307 Chirality : 0.043 0.179 978 Planarity : 0.005 0.037 1176 Dihedral : 5.311 50.798 1013 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.71 % Allowed : 8.29 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 793 helix: 1.13 (0.25), residues: 388 sheet: 0.79 (0.74), residues: 43 loop : -0.15 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.003 0.001 HIS E 378 PHE 0.015 0.001 PHE E 523 TYR 0.025 0.001 TYR E 50 ARG 0.006 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 3.04662 ( 21) hydrogen bonds : bond 0.04359 ( 319) hydrogen bonds : angle 4.54180 ( 906) SS BOND : bond 0.00424 ( 6) SS BOND : angle 2.28134 ( 12) covalent geometry : bond 0.00410 ( 6737) covalent geometry : angle 0.57591 ( 9155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8599 (mt-10) REVERT: B 498 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8793 (mm-40) REVERT: E 270 MET cc_start: 0.9210 (tpp) cc_final: 0.8801 (tpp) REVERT: E 323 MET cc_start: 0.9408 (mmp) cc_final: 0.9082 (mmm) REVERT: E 332 MET cc_start: 0.8917 (ptm) cc_final: 0.8663 (ttp) REVERT: E 360 MET cc_start: 0.8442 (tpt) cc_final: 0.8134 (tmm) REVERT: E 368 ASP cc_start: 0.8996 (m-30) cc_final: 0.8525 (t0) REVERT: E 429 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8043 (tm-30) REVERT: E 471 ASP cc_start: 0.9039 (p0) cc_final: 0.8773 (t0) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.1400 time to fit residues: 12.6520 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5106 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.062988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.046795 restraints weight = 22776.678| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.02 r_work: 0.2604 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6750 Z= 0.113 Angle : 0.510 5.695 9188 Z= 0.260 Chirality : 0.040 0.151 978 Planarity : 0.004 0.037 1176 Dihedral : 4.875 53.493 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.57 % Allowed : 9.43 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 793 helix: 1.69 (0.26), residues: 380 sheet: 0.53 (0.72), residues: 43 loop : -0.01 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.015 0.001 TYR E 50 ARG 0.004 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 7) link_NAG-ASN : angle 2.50543 ( 21) hydrogen bonds : bond 0.03802 ( 319) hydrogen bonds : angle 4.27035 ( 906) SS BOND : bond 0.00442 ( 6) SS BOND : angle 2.10893 ( 12) covalent geometry : bond 0.00242 ( 6737) covalent geometry : angle 0.49056 ( 9155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.9167 (m-30) cc_final: 0.8956 (p0) REVERT: B 406 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8702 (mt-10) REVERT: B 498 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8670 (mm-40) REVERT: E 82 MET cc_start: 0.9107 (mtp) cc_final: 0.8874 (mtp) REVERT: E 123 MET cc_start: 0.8881 (mmm) cc_final: 0.8665 (mmt) REVERT: E 142 LEU cc_start: 0.9460 (mm) cc_final: 0.9165 (tp) REVERT: E 270 MET cc_start: 0.9058 (tpp) cc_final: 0.8534 (tpp) REVERT: E 323 MET cc_start: 0.9521 (mmp) cc_final: 0.9066 (mmm) REVERT: E 332 MET cc_start: 0.8962 (ptm) cc_final: 0.8705 (ttp) REVERT: E 360 MET cc_start: 0.8275 (tpt) cc_final: 0.8018 (tmm) REVERT: E 368 ASP cc_start: 0.8830 (m-30) cc_final: 0.8561 (t0) outliers start: 4 outliers final: 0 residues processed: 57 average time/residue: 0.1260 time to fit residues: 11.3163 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.063600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047909 restraints weight = 22574.453| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.89 r_work: 0.2626 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6750 Z= 0.100 Angle : 0.477 5.328 9188 Z= 0.246 Chirality : 0.039 0.137 978 Planarity : 0.003 0.035 1176 Dihedral : 4.651 54.521 1013 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.29 % Allowed : 9.43 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.30), residues: 793 helix: 1.81 (0.26), residues: 388 sheet: 0.55 (0.73), residues: 43 loop : 0.17 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.002 0.001 HIS E 374 PHE 0.012 0.001 PHE E 369 TYR 0.015 0.001 TYR E 50 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 2.18929 ( 21) hydrogen bonds : bond 0.03551 ( 319) hydrogen bonds : angle 4.10287 ( 906) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.35149 ( 12) covalent geometry : bond 0.00216 ( 6737) covalent geometry : angle 0.46387 ( 9155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8751 (mt-10) REVERT: E 270 MET cc_start: 0.8967 (tpp) cc_final: 0.8420 (tpp) REVERT: E 462 MET cc_start: 0.9620 (mtm) cc_final: 0.9276 (mtm) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.1325 time to fit residues: 10.6130 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.062284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.046590 restraints weight = 22476.440| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.83 r_work: 0.2636 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6750 Z= 0.130 Angle : 0.491 5.735 9188 Z= 0.252 Chirality : 0.040 0.142 978 Planarity : 0.003 0.036 1176 Dihedral : 4.580 54.787 1013 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 9.86 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.30), residues: 793 helix: 2.00 (0.26), residues: 385 sheet: 0.60 (0.74), residues: 43 loop : 0.41 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.002 0.001 HIS E 374 PHE 0.012 0.001 PHE E 369 TYR 0.016 0.001 TYR E 50 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 7) link_NAG-ASN : angle 2.08096 ( 21) hydrogen bonds : bond 0.03673 ( 319) hydrogen bonds : angle 4.08254 ( 906) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.06564 ( 12) covalent geometry : bond 0.00287 ( 6737) covalent geometry : angle 0.48003 ( 9155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8763 (mt-10) REVERT: B 498 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8893 (mm-40) REVERT: E 267 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9293 (mm) REVERT: E 270 MET cc_start: 0.8889 (tpp) cc_final: 0.8315 (tpp) REVERT: E 368 ASP cc_start: 0.9051 (m-30) cc_final: 0.8515 (t0) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1381 time to fit residues: 11.0615 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.062606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.046930 restraints weight = 22382.604| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.84 r_work: 0.2637 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6750 Z= 0.114 Angle : 0.473 5.356 9188 Z= 0.243 Chirality : 0.040 0.139 978 Planarity : 0.003 0.035 1176 Dihedral : 4.492 55.666 1013 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 9.57 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.30), residues: 793 helix: 2.04 (0.26), residues: 385 sheet: 0.57 (0.74), residues: 43 loop : 0.47 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE E 369 TYR 0.014 0.001 TYR E 50 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 7) link_NAG-ASN : angle 1.96697 ( 21) hydrogen bonds : bond 0.03542 ( 319) hydrogen bonds : angle 4.06342 ( 906) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.94666 ( 12) covalent geometry : bond 0.00250 ( 6737) covalent geometry : angle 0.46275 ( 9155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8824 (mt-10) REVERT: B 498 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8884 (mm-40) REVERT: E 23 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9112 (pt0) REVERT: E 86 GLN cc_start: 0.9096 (pm20) cc_final: 0.8772 (pm20) REVERT: E 267 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9267 (mm) REVERT: E 270 MET cc_start: 0.8849 (tpp) cc_final: 0.8232 (tpp) REVERT: E 323 MET cc_start: 0.9252 (mmm) cc_final: 0.8975 (mmm) REVERT: E 360 MET cc_start: 0.8084 (tmm) cc_final: 0.7195 (tmm) REVERT: E 368 ASP cc_start: 0.9071 (m-30) cc_final: 0.8487 (t0) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.1356 time to fit residues: 11.6147 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.061102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.045475 restraints weight = 22591.016| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.83 r_work: 0.2590 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6750 Z= 0.166 Angle : 0.519 6.509 9188 Z= 0.264 Chirality : 0.041 0.152 978 Planarity : 0.004 0.044 1176 Dihedral : 4.574 55.172 1013 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.29 % Allowed : 10.29 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.30), residues: 793 helix: 2.02 (0.26), residues: 385 sheet: 0.22 (0.72), residues: 45 loop : 0.53 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.014 0.001 TYR B 453 ARG 0.006 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 1.99088 ( 21) hydrogen bonds : bond 0.03798 ( 319) hydrogen bonds : angle 4.16062 ( 906) SS BOND : bond 0.00164 ( 6) SS BOND : angle 1.02157 ( 12) covalent geometry : bond 0.00367 ( 6737) covalent geometry : angle 0.50969 ( 9155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8884 (mt-10) REVERT: B 442 ASP cc_start: 0.9074 (m-30) cc_final: 0.8834 (m-30) REVERT: B 498 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8770 (mm-40) REVERT: B 518 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7158 (tt) REVERT: E 82 MET cc_start: 0.9224 (mtp) cc_final: 0.8777 (ttp) REVERT: E 86 GLN cc_start: 0.9148 (pm20) cc_final: 0.8813 (pm20) REVERT: E 267 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9289 (mm) REVERT: E 270 MET cc_start: 0.8733 (tpp) cc_final: 0.8046 (tpp) REVERT: E 332 MET cc_start: 0.9002 (ttp) cc_final: 0.8563 (ppp) REVERT: E 360 MET cc_start: 0.8145 (tmm) cc_final: 0.7520 (tmm) REVERT: E 368 ASP cc_start: 0.9156 (m-30) cc_final: 0.8620 (t0) REVERT: E 474 MET cc_start: 0.9085 (mmp) cc_final: 0.8876 (mmm) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1258 time to fit residues: 10.9632 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.061557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046003 restraints weight = 22706.361| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.85 r_work: 0.2607 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6750 Z= 0.127 Angle : 0.494 5.906 9188 Z= 0.252 Chirality : 0.040 0.142 978 Planarity : 0.003 0.034 1176 Dihedral : 4.509 56.034 1013 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 10.71 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.30), residues: 793 helix: 1.99 (0.26), residues: 391 sheet: 0.40 (0.73), residues: 43 loop : 0.59 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.011 0.001 PHE E 369 TYR 0.015 0.001 TYR E 50 ARG 0.005 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 7) link_NAG-ASN : angle 1.95200 ( 21) hydrogen bonds : bond 0.03639 ( 319) hydrogen bonds : angle 4.12105 ( 906) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.92326 ( 12) covalent geometry : bond 0.00279 ( 6737) covalent geometry : angle 0.48486 ( 9155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8912 (mt-10) REVERT: B 442 ASP cc_start: 0.9053 (m-30) cc_final: 0.8815 (m-30) REVERT: B 498 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8862 (mm-40) REVERT: B 518 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7224 (tt) REVERT: E 82 MET cc_start: 0.9192 (mtp) cc_final: 0.8796 (ttp) REVERT: E 86 GLN cc_start: 0.9113 (pm20) cc_final: 0.8778 (pm20) REVERT: E 267 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9280 (mm) REVERT: E 270 MET cc_start: 0.8701 (tpp) cc_final: 0.8020 (tpp) REVERT: E 332 MET cc_start: 0.8971 (ttp) cc_final: 0.8634 (ppp) REVERT: E 360 MET cc_start: 0.8035 (tmm) cc_final: 0.7511 (tmm) REVERT: E 368 ASP cc_start: 0.9115 (m-30) cc_final: 0.8573 (t0) REVERT: E 480 MET cc_start: 0.9253 (mtp) cc_final: 0.8981 (mtp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.1375 time to fit residues: 11.4651 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.0060 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.062551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.046783 restraints weight = 22585.722| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.90 r_work: 0.2626 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6750 Z= 0.114 Angle : 0.485 6.907 9188 Z= 0.248 Chirality : 0.040 0.136 978 Planarity : 0.003 0.034 1176 Dihedral : 4.435 56.379 1013 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.14 % Allowed : 10.57 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.30), residues: 793 helix: 2.02 (0.26), residues: 391 sheet: 0.16 (0.72), residues: 45 loop : 0.59 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.011 0.001 PHE E 369 TYR 0.017 0.001 TYR E 50 ARG 0.005 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 7) link_NAG-ASN : angle 1.93614 ( 21) hydrogen bonds : bond 0.03540 ( 319) hydrogen bonds : angle 4.09459 ( 906) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.87550 ( 12) covalent geometry : bond 0.00250 ( 6737) covalent geometry : angle 0.47593 ( 9155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 ASP cc_start: 0.9030 (m-30) cc_final: 0.8813 (m-30) REVERT: B 498 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8876 (mm-40) REVERT: B 518 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7214 (tt) REVERT: E 82 MET cc_start: 0.9161 (mtp) cc_final: 0.8784 (ttp) REVERT: E 86 GLN cc_start: 0.9119 (pm20) cc_final: 0.8777 (pm20) REVERT: E 267 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9265 (mm) REVERT: E 270 MET cc_start: 0.8674 (tpp) cc_final: 0.8002 (tpp) REVERT: E 332 MET cc_start: 0.8920 (ttp) cc_final: 0.8568 (ppp) REVERT: E 360 MET cc_start: 0.7944 (tmm) cc_final: 0.7397 (tmm) REVERT: E 368 ASP cc_start: 0.9081 (m-30) cc_final: 0.8560 (t0) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.1406 time to fit residues: 12.1431 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.062129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.046316 restraints weight = 22877.503| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.92 r_work: 0.2610 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6750 Z= 0.140 Angle : 0.513 6.893 9188 Z= 0.261 Chirality : 0.041 0.152 978 Planarity : 0.003 0.034 1176 Dihedral : 4.487 56.028 1013 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.14 % Allowed : 10.86 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.30), residues: 793 helix: 2.01 (0.26), residues: 390 sheet: 0.12 (0.70), residues: 45 loop : 0.66 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE E 369 TYR 0.019 0.001 TYR E 50 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 7) link_NAG-ASN : angle 1.95875 ( 21) hydrogen bonds : bond 0.03672 ( 319) hydrogen bonds : angle 4.16993 ( 906) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.90447 ( 12) covalent geometry : bond 0.00310 ( 6737) covalent geometry : angle 0.50381 ( 9155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8887 (p0) cc_final: 0.8233 (p0) REVERT: B 406 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: B 498 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8804 (mm-40) REVERT: B 518 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7216 (tt) REVERT: E 82 MET cc_start: 0.9192 (mtp) cc_final: 0.8808 (ttp) REVERT: E 86 GLN cc_start: 0.9157 (pm20) cc_final: 0.8809 (pm20) REVERT: E 267 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9279 (mm) REVERT: E 270 MET cc_start: 0.8660 (tpp) cc_final: 0.7988 (tpp) REVERT: E 332 MET cc_start: 0.8945 (ttp) cc_final: 0.8571 (ppp) REVERT: E 360 MET cc_start: 0.7882 (tmm) cc_final: 0.7327 (tmm) REVERT: E 368 ASP cc_start: 0.9038 (m-30) cc_final: 0.8519 (t0) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.1436 time to fit residues: 11.4097 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 65 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.062593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.046763 restraints weight = 22807.267| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.95 r_work: 0.2610 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6750 Z= 0.103 Angle : 0.490 6.604 9188 Z= 0.249 Chirality : 0.040 0.145 978 Planarity : 0.003 0.034 1176 Dihedral : 4.377 56.922 1013 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 11.43 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.30), residues: 793 helix: 2.06 (0.26), residues: 384 sheet: 0.13 (0.71), residues: 45 loop : 0.68 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE E 369 TYR 0.018 0.001 TYR E 50 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.93122 ( 21) hydrogen bonds : bond 0.03439 ( 319) hydrogen bonds : angle 4.12699 ( 906) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.82893 ( 12) covalent geometry : bond 0.00224 ( 6737) covalent geometry : angle 0.48156 ( 9155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.85 seconds wall clock time: 60 minutes 15.27 seconds (3615.27 seconds total)