Starting phenix.real_space_refine on Thu Jul 24 22:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.map" model { file = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2025/7tez_25856.cif" } resolution = 3.27 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= 0.014 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 4186 2.51 5 N 1082 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 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: 5.06, per 1000 atoms: 0.77 Number of scatterers: 6553 At special positions: 0 Unit cell: (81, 84, 121, 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 1248 8.00 N 1082 7.00 C 4186 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=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.02 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: 1.33 Conformation dependent library (CDL) restraints added in 841.9 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: 40 helices and 7 sheets defined 57.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.713A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.084A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.747A 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: 4.084A 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: 3.970A 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: 3.694A 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: 3.745A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.766A 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: 3.558A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.667A 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: 4.292A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.514A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.312A 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: 3.596A 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: 4.494A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.829A 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: 4.013A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.811A 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: 6.093A 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: 6.377A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 912 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: 1.73 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.47: 1765 1.47 - 1.59: 2827 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 8789 2.06 - 4.11: 320 4.11 - 6.17: 32 6.17 - 8.22: 8 8.22 - 10.28: 3 Bond angle restraints: 9152 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.51 -6.15 1.42e+00 4.96e-01 1.87e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 122.85 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 122.38 115.83 6.55 1.81e+00 3.05e-01 1.31e+01 angle pdb=" CA LYS E 31 " pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 3676 16.72 - 33.43: 308 33.43 - 50.15: 56 50.15 - 66.87: 16 66.87 - 83.58: 12 Dihedral angle restraints: 4068 sinusoidal: 1730 harmonic: 2338 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 -48.44 -37.56 1 1.00e+01 1.00e-02 1.99e+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 16.07 62.93 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual 122.80 130.82 -8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 4065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 726 0.061 - 0.121: 205 0.121 - 0.182: 38 0.182 - 0.243: 6 0.243 - 0.303: 2 Chirality restraints: 977 Sorted by residual: chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 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 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.056 5.00e-02 4.00e+02 8.31e-02 1.11e+01 pdb=" N PRO E 590 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO E 500 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 478 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO B 479 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.034 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2097 2.84 - 3.35: 5957 3.35 - 3.87: 11286 3.87 - 4.38: 12699 4.38 - 4.90: 22030 Nonbonded interactions: 54069 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.323 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.344 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.360 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.366 3.120 ... (remaining 54064 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: 4.230 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.140 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 6748 Z= 0.256 Angle : 0.922 11.310 9185 Z= 0.516 Chirality : 0.060 0.303 977 Planarity : 0.008 0.083 1178 Dihedral : 13.451 83.585 2550 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.71 % Allowed : 2.57 % Favored : 96.71 % 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: 0.05 (0.25), residues: 793 helix: 0.58 (0.22), residues: 392 sheet: 1.01 (0.72), residues: 43 loop : -0.62 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 69 HIS 0.013 0.002 HIS E 34 PHE 0.028 0.003 PHE E 369 TYR 0.041 0.003 TYR B 495 ARG 0.014 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 7) link_NAG-ASN : angle 4.32550 ( 21) hydrogen bonds : bond 0.14602 ( 323) hydrogen bonds : angle 6.06242 ( 912) SS BOND : bond 0.00665 ( 6) SS BOND : angle 2.43294 ( 12) covalent geometry : bond 0.00551 ( 6735) covalent geometry : angle 0.89558 ( 9152) *********************** 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 153 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.777 Fit side-chains REVERT: B 417 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8826 (mmtm) REVERT: B 470 THR cc_start: 0.8859 (p) cc_final: 0.8567 (t) REVERT: E 291 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 436 ILE cc_start: 0.9036 (mm) cc_final: 0.8812 (mt) REVERT: E 475 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8002 (tptp) REVERT: E 483 GLU cc_start: 0.8717 (tp30) cc_final: 0.8452 (tp30) outliers start: 5 outliers final: 0 residues processed: 151 average time/residue: 0.2362 time to fit residues: 45.1460 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 ILE 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN E 345 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065403 restraints weight = 17040.109| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.26 r_work: 0.2831 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6748 Z= 0.215 Angle : 0.623 7.708 9185 Z= 0.316 Chirality : 0.044 0.157 977 Planarity : 0.005 0.037 1178 Dihedral : 5.730 52.375 1015 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 9.00 % Favored : 89.71 % 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: 1.15 (0.28), residues: 793 helix: 1.46 (0.25), residues: 389 sheet: 0.87 (0.73), residues: 42 loop : 0.09 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.008 0.002 HIS E 34 PHE 0.018 0.002 PHE E 428 TYR 0.016 0.001 TYR E 385 ARG 0.004 0.001 ARG E 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 2.76209 ( 21) hydrogen bonds : bond 0.04561 ( 323) hydrogen bonds : angle 4.63793 ( 912) SS BOND : bond 0.00430 ( 6) SS BOND : angle 1.67669 ( 12) covalent geometry : bond 0.00477 ( 6735) covalent geometry : angle 0.60740 ( 9152) *********************** 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.9249 (p) cc_final: 0.8889 (t) REVERT: B 506 GLN cc_start: 0.9272 (mt0) cc_final: 0.8762 (mt0) REVERT: E 483 GLU cc_start: 0.8979 (tp30) cc_final: 0.8680 (tp30) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.1907 time to fit residues: 19.6937 Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 chunk 71 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3336 r_free = 0.3336 target = 0.084530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067316 restraints weight = 17131.941| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.38 r_work: 0.2868 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6748 Z= 0.116 Angle : 0.516 5.997 9185 Z= 0.261 Chirality : 0.040 0.159 977 Planarity : 0.004 0.040 1178 Dihedral : 5.102 53.801 1013 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.71 % Allowed : 11.00 % 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: 1.46 (0.29), residues: 793 helix: 1.73 (0.26), residues: 387 sheet: 0.69 (0.73), residues: 42 loop : 0.27 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.006 0.001 HIS E 34 PHE 0.015 0.001 PHE E 428 TYR 0.013 0.001 TYR E 385 ARG 0.002 0.000 ARG E 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 7) link_NAG-ASN : angle 2.30416 ( 21) hydrogen bonds : bond 0.03927 ( 323) hydrogen bonds : angle 4.37830 ( 912) SS BOND : bond 0.00377 ( 6) SS BOND : angle 1.54458 ( 12) covalent geometry : bond 0.00255 ( 6735) covalent geometry : angle 0.50150 ( 9152) *********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.9213 (p) cc_final: 0.8814 (t) REVERT: B 506 GLN cc_start: 0.9287 (mt0) cc_final: 0.8745 (mt0) REVERT: E 376 MET cc_start: 0.9077 (ttm) cc_final: 0.8802 (tpp) REVERT: E 483 GLU cc_start: 0.8982 (tp30) cc_final: 0.8663 (tp30) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1726 time to fit residues: 19.3677 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.064512 restraints weight = 17373.665| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.35 r_work: 0.2811 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6748 Z= 0.186 Angle : 0.562 9.965 9185 Z= 0.281 Chirality : 0.042 0.153 977 Planarity : 0.004 0.041 1178 Dihedral : 5.236 54.663 1013 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.43 % Allowed : 11.00 % Favored : 87.57 % 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: 1.52 (0.30), residues: 793 helix: 1.68 (0.26), residues: 392 sheet: 0.68 (0.73), residues: 42 loop : 0.43 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.006 0.001 HIS E 34 PHE 0.015 0.001 PHE E 369 TYR 0.016 0.001 TYR E 385 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 7) link_NAG-ASN : angle 2.08394 ( 21) hydrogen bonds : bond 0.04165 ( 323) hydrogen bonds : angle 4.34079 ( 912) SS BOND : bond 0.00364 ( 6) SS BOND : angle 1.28765 ( 12) covalent geometry : bond 0.00418 ( 6735) covalent geometry : angle 0.55252 ( 9152) *********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.9254 (p) cc_final: 0.8801 (t) REVERT: B 506 GLN cc_start: 0.9275 (mt0) cc_final: 0.8759 (mt0) REVERT: E 190 MET cc_start: 0.8803 (tmm) cc_final: 0.8579 (tmm) REVERT: E 376 MET cc_start: 0.9070 (ttm) cc_final: 0.8736 (tpp) REVERT: E 483 GLU cc_start: 0.8974 (tp30) cc_final: 0.8680 (tp30) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.1889 time to fit residues: 20.3586 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.083107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.066274 restraints weight = 17215.690| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.22 r_work: 0.2855 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.144 Angle : 0.525 8.275 9185 Z= 0.262 Chirality : 0.041 0.153 977 Planarity : 0.003 0.041 1178 Dihedral : 5.088 55.301 1013 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 12.43 % Favored : 86.71 % 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: 1.50 (0.30), residues: 793 helix: 1.60 (0.26), residues: 400 sheet: 0.58 (0.72), residues: 42 loop : 0.48 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 PHE 0.013 0.001 PHE E 369 TYR 0.014 0.001 TYR E 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 7) link_NAG-ASN : angle 1.98353 ( 21) hydrogen bonds : bond 0.03928 ( 323) hydrogen bonds : angle 4.25973 ( 912) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.19055 ( 12) covalent geometry : bond 0.00325 ( 6735) covalent geometry : angle 0.51558 ( 9152) *********************** 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 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.9096 (p) cc_final: 0.8639 (t) REVERT: B 506 GLN cc_start: 0.9262 (mt0) cc_final: 0.8787 (mt0) REVERT: E 190 MET cc_start: 0.8870 (tmm) cc_final: 0.8656 (tmm) REVERT: E 376 MET cc_start: 0.9078 (ttm) cc_final: 0.8814 (tpp) REVERT: E 483 GLU cc_start: 0.8970 (tp30) cc_final: 0.8670 (tp30) REVERT: E 586 ASN cc_start: 0.8977 (t0) cc_final: 0.8656 (t0) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.1806 time to fit residues: 19.0455 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.082706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.065990 restraints weight = 17086.387| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.21 r_work: 0.2850 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6748 Z= 0.145 Angle : 0.515 7.849 9185 Z= 0.258 Chirality : 0.041 0.152 977 Planarity : 0.003 0.042 1178 Dihedral : 5.007 55.745 1013 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.00 % Allowed : 12.86 % Favored : 86.14 % 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: 1.66 (0.30), residues: 793 helix: 1.74 (0.26), residues: 392 sheet: 0.62 (0.73), residues: 42 loop : 0.59 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 610 HIS 0.004 0.001 HIS E 34 PHE 0.013 0.001 PHE E 369 TYR 0.013 0.001 TYR E 385 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 7) link_NAG-ASN : angle 1.88348 ( 21) hydrogen bonds : bond 0.03861 ( 323) hydrogen bonds : angle 4.23567 ( 912) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.05114 ( 12) covalent geometry : bond 0.00326 ( 6735) covalent geometry : angle 0.50652 ( 9152) *********************** 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 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9273 (mt0) cc_final: 0.8796 (mt0) REVERT: E 190 MET cc_start: 0.8889 (tmm) cc_final: 0.8660 (tmm) REVERT: E 376 MET cc_start: 0.9077 (ttm) cc_final: 0.8859 (tpp) REVERT: E 483 GLU cc_start: 0.8951 (tp30) cc_final: 0.8673 (tp30) REVERT: E 586 ASN cc_start: 0.8980 (t0) cc_final: 0.8664 (t0) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1845 time to fit residues: 19.5081 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.082971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066264 restraints weight = 17209.044| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.20 r_work: 0.2855 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6748 Z= 0.134 Angle : 0.506 7.541 9185 Z= 0.254 Chirality : 0.041 0.152 977 Planarity : 0.003 0.039 1178 Dihedral : 4.918 56.005 1013 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 12.57 % Favored : 86.29 % 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: 1.68 (0.30), residues: 793 helix: 1.73 (0.26), residues: 392 sheet: 0.62 (0.73), residues: 42 loop : 0.64 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 610 HIS 0.004 0.001 HIS E 34 PHE 0.010 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 7) link_NAG-ASN : angle 1.84633 ( 21) hydrogen bonds : bond 0.03802 ( 323) hydrogen bonds : angle 4.21697 ( 912) SS BOND : bond 0.00324 ( 6) SS BOND : angle 1.01349 ( 12) covalent geometry : bond 0.00301 ( 6735) covalent geometry : angle 0.49829 ( 9152) *********************** 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 424 LYS cc_start: 0.9125 (tppt) cc_final: 0.8849 (tppt) REVERT: E 190 MET cc_start: 0.8885 (tmm) cc_final: 0.8655 (tmm) REVERT: E 483 GLU cc_start: 0.8945 (tp30) cc_final: 0.8667 (tp30) REVERT: E 586 ASN cc_start: 0.8909 (t0) cc_final: 0.8577 (t0) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.2073 time to fit residues: 21.8670 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.083868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067035 restraints weight = 17200.293| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.24 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6748 Z= 0.114 Angle : 0.506 6.864 9185 Z= 0.253 Chirality : 0.040 0.170 977 Planarity : 0.003 0.038 1178 Dihedral : 4.802 56.151 1013 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 12.86 % Favored : 85.86 % 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: 1.72 (0.30), residues: 793 helix: 1.74 (0.26), residues: 392 sheet: 0.62 (0.75), residues: 42 loop : 0.68 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 610 HIS 0.003 0.001 HIS E 239 PHE 0.011 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 7) link_NAG-ASN : angle 1.80011 ( 21) hydrogen bonds : bond 0.03671 ( 323) hydrogen bonds : angle 4.19100 ( 912) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.00437 ( 12) covalent geometry : bond 0.00253 ( 6735) covalent geometry : angle 0.49834 ( 9152) *********************** 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8661 (mt-10) REVERT: B 424 LYS cc_start: 0.9117 (tppt) cc_final: 0.8847 (tppt) REVERT: E 190 MET cc_start: 0.8886 (tmm) cc_final: 0.8656 (tmm) REVERT: E 483 GLU cc_start: 0.8976 (tp30) cc_final: 0.8673 (tp30) REVERT: E 586 ASN cc_start: 0.8850 (t0) cc_final: 0.8516 (t0) outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.1928 time to fit residues: 20.3448 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 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 = 0.3317 r_free = 0.3317 target = 0.083026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066155 restraints weight = 17313.855| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.22 r_work: 0.2854 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.141 Angle : 0.522 7.173 9185 Z= 0.261 Chirality : 0.041 0.160 977 Planarity : 0.003 0.037 1178 Dihedral : 4.861 56.320 1013 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 13.14 % Favored : 85.71 % 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: 1.71 (0.30), residues: 793 helix: 1.75 (0.26), residues: 392 sheet: 0.25 (0.74), residues: 44 loop : 0.71 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 610 HIS 0.004 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.013 0.001 TYR E 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 1.81801 ( 21) hydrogen bonds : bond 0.03802 ( 323) hydrogen bonds : angle 4.19991 ( 912) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.92696 ( 12) covalent geometry : bond 0.00316 ( 6735) covalent geometry : angle 0.51490 ( 9152) *********************** 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 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8813 (mt-10) cc_final: 0.7978 (tm-30) REVERT: B 406 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8706 (mt-10) REVERT: E 190 MET cc_start: 0.8887 (tmm) cc_final: 0.8652 (tmm) REVERT: E 323 MET cc_start: 0.8851 (mmm) cc_final: 0.8119 (mmm) REVERT: E 483 GLU cc_start: 0.8986 (tp30) cc_final: 0.8677 (tp30) REVERT: E 586 ASN cc_start: 0.8933 (t0) cc_final: 0.8602 (t0) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.2010 time to fit residues: 20.2337 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.084242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067407 restraints weight = 17314.213| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.24 r_work: 0.2878 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6748 Z= 0.112 Angle : 0.506 6.914 9185 Z= 0.252 Chirality : 0.040 0.157 977 Planarity : 0.003 0.038 1178 Dihedral : 4.687 56.341 1013 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.00 % Allowed : 13.43 % Favored : 85.57 % 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: 1.77 (0.30), residues: 793 helix: 1.77 (0.26), residues: 392 sheet: 0.66 (0.75), residues: 42 loop : 0.72 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 610 HIS 0.003 0.001 HIS E 374 PHE 0.010 0.001 PHE E 315 TYR 0.010 0.001 TYR E 385 ARG 0.001 0.000 ARG E 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 7) link_NAG-ASN : angle 1.81357 ( 21) hydrogen bonds : bond 0.03602 ( 323) hydrogen bonds : angle 4.16152 ( 912) SS BOND : bond 0.00277 ( 6) SS BOND : angle 0.95267 ( 12) covalent geometry : bond 0.00246 ( 6735) covalent geometry : angle 0.49842 ( 9152) ********************** 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8028 (tm-30) REVERT: E 190 MET cc_start: 0.8878 (tmm) cc_final: 0.8650 (tmm) REVERT: E 323 MET cc_start: 0.8774 (mmm) cc_final: 0.7846 (mmm) REVERT: E 483 GLU cc_start: 0.8974 (tp30) cc_final: 0.8666 (tp30) REVERT: E 586 ASN cc_start: 0.8852 (t0) cc_final: 0.8500 (t0) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1710 time to fit residues: 17.3095 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.083691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066677 restraints weight = 17458.308| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.28 r_work: 0.2859 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.129 Angle : 0.512 6.999 9185 Z= 0.256 Chirality : 0.041 0.155 977 Planarity : 0.004 0.039 1178 Dihedral : 4.723 56.414 1013 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 13.57 % Favored : 85.57 % 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: 1.79 (0.30), residues: 793 helix: 1.77 (0.26), residues: 393 sheet: 0.67 (0.75), residues: 42 loop : 0.75 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 610 HIS 0.004 0.001 HIS E 239 PHE 0.011 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.001 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 7) link_NAG-ASN : angle 1.78879 ( 21) hydrogen bonds : bond 0.03704 ( 323) hydrogen bonds : angle 4.15466 ( 912) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.91839 ( 12) covalent geometry : bond 0.00290 ( 6735) covalent geometry : angle 0.50479 ( 9152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.99 seconds wall clock time: 57 minutes 10.38 seconds (3430.38 seconds total)