Starting phenix.real_space_refine on Sun Apr 27 18:23:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyo_38779/04_2025/8xyo_38779.cif" } resolution = 3.04 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 4074 2.51 5 N 1047 2.21 5 O 1212 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-5669/modules/chem_data/mon_lib" Total number of atoms: 6369 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 578, 4729 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 24, 'TRANS': 553} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 578, 4729 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 24, 'TRANS': 553} Chain breaks: 1 bond proxies already assigned to first conformer: 4850 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 7.19, per 1000 atoms: 1.13 Number of scatterers: 6369 At special positions: 0 Unit cell: (73.95, 93.5, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 1212 8.00 N 1047 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 103 " " NAG A 704 " - " ASN A 53 " " NAG A 705 " - " ASN A 322 " " NAG A 706 " - " ASN A 432 " " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 707 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 374 " 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 58.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.703A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.783A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.919A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.835A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.765A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.023A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.611A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 281 removed outlier: 4.162A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.735A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.850A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.686A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.055A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.524A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.882A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.716A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.543A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' 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 389 removed outlier: 4.156A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.344A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 313 hydrogen bonds defined for protein. 874 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: 1.49 Time building geometry restraints manager: 1.89 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: 2025 1.34 - 1.46: 1534 1.46 - 1.58: 2932 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 6547 Sorted by residual: bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C TYR B 495 " pdb=" N GLY B 496 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.13e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C1 NAG A 706 " pdb=" O5 NAG A 706 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 ... (remaining 6542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8478 1.25 - 2.49: 327 2.49 - 3.74: 71 3.74 - 4.99: 19 4.99 - 6.23: 2 Bond angle restraints: 8897 Sorted by residual: angle pdb=" C THR A 334 " pdb=" N ASP A 335 " pdb=" CA ASP A 335 " ideal model delta sigma weight residual 121.20 125.70 -4.50 1.40e+00 5.10e-01 1.03e+01 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 113.25 116.69 -3.44 1.30e+00 5.92e-01 7.02e+00 angle pdb=" C PRO A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" C TYR B 495 " pdb=" N GLY B 496 " pdb=" CA GLY B 496 " ideal model delta sigma weight residual 122.29 120.31 1.98 8.90e-01 1.26e+00 4.93e+00 angle pdb=" CA TRP A 165 " pdb=" CB TRP A 165 " pdb=" CG TRP A 165 " ideal model delta sigma weight residual 113.60 117.33 -3.73 1.90e+00 2.77e-01 3.86e+00 ... (remaining 8892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3590 17.79 - 35.57: 271 35.57 - 53.36: 48 53.36 - 71.14: 12 71.14 - 88.93: 14 Dihedral angle restraints: 3935 sinusoidal: 1669 harmonic: 2266 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 173.04 -80.04 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -48.28 -37.72 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.30 -36.30 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 508 0.028 - 0.056: 292 0.056 - 0.085: 91 0.085 - 0.113: 47 0.113 - 0.141: 11 Chirality restraints: 949 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 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 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 946 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 475 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C LYS A 475 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS A 475 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 476 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C TRP A 473 " 0.026 2.00e-02 2.50e+03 pdb=" O TRP A 473 " -0.010 2.00e-02 2.50e+03 pdb=" N MET A 474 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 336 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.020 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 69 2.66 - 3.22: 5794 3.22 - 3.78: 9374 3.78 - 4.34: 12820 4.34 - 4.90: 21900 Nonbonded interactions: 49957 Sorted by model distance: nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.097 2.460 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.098 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.105 2.230 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.205 3.040 nonbonded pdb=" O ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.227 3.040 ... (remaining 49952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.070 Process input model: 23.400 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 0.202 6560 Z= 0.225 Angle : 0.607 7.932 8926 Z= 0.323 Chirality : 0.042 0.141 949 Planarity : 0.004 0.037 1141 Dihedral : 13.686 88.931 2471 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.30), residues: 768 helix: 1.20 (0.27), residues: 395 sheet: 0.42 (0.66), residues: 60 loop : -1.05 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.017 0.002 PHE A 512 TYR 0.016 0.001 TYR A 158 ARG 0.003 0.000 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 2.73806 ( 21) hydrogen bonds : bond 0.16064 ( 313) hydrogen bonds : angle 5.81376 ( 874) metal coordination : bond 0.20153 ( 2) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.60120 ( 8) covalent geometry : bond 0.00416 ( 6547) covalent geometry : angle 0.59324 ( 8897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7343 (tt0) cc_final: 0.7074 (tt0) REVERT: A 231 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 243 TYR cc_start: 0.7578 (t80) cc_final: 0.7359 (t80) REVERT: A 299 ASP cc_start: 0.8028 (m-30) cc_final: 0.7727 (m-30) REVERT: A 435 GLU cc_start: 0.7294 (mp0) cc_final: 0.6706 (mp0) REVERT: A 491 VAL cc_start: 0.8438 (t) cc_final: 0.8130 (p) REVERT: A 512 PHE cc_start: 0.8588 (t80) cc_final: 0.8384 (t80) REVERT: A 515 TYR cc_start: 0.8382 (m-80) cc_final: 0.7475 (m-80) REVERT: A 564 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7257 (mm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1836 time to fit residues: 38.8155 Evaluate side-chains 137 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 524 GLN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101795 restraints weight = 19447.419| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.45 r_work: 0.3177 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6560 Z= 0.205 Angle : 0.617 8.300 8926 Z= 0.319 Chirality : 0.045 0.206 949 Planarity : 0.004 0.038 1141 Dihedral : 6.178 55.037 988 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.03 % Allowed : 6.78 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.30), residues: 768 helix: 1.39 (0.27), residues: 386 sheet: 0.27 (0.66), residues: 61 loop : -1.12 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 165 HIS 0.008 0.002 HIS A 401 PHE 0.020 0.002 PHE A 512 TYR 0.015 0.002 TYR A 158 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 7) link_NAG-ASN : angle 3.23584 ( 21) hydrogen bonds : bond 0.06893 ( 313) hydrogen bonds : angle 4.46984 ( 874) metal coordination : bond 0.00357 ( 2) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.45079 ( 8) covalent geometry : bond 0.00482 ( 6547) covalent geometry : angle 0.59660 ( 8897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8278 (tttt) cc_final: 0.8057 (tttt) REVERT: A 75 GLU cc_start: 0.7714 (tt0) cc_final: 0.7457 (tt0) REVERT: A 202 TYR cc_start: 0.8474 (t80) cc_final: 0.8112 (t80) REVERT: A 231 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 243 TYR cc_start: 0.7490 (t80) cc_final: 0.7206 (t80) REVERT: A 299 ASP cc_start: 0.7876 (m-30) cc_final: 0.7613 (m-30) REVERT: A 435 GLU cc_start: 0.7332 (mp0) cc_final: 0.6838 (mp0) REVERT: A 474 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: A 491 VAL cc_start: 0.8406 (t) cc_final: 0.8081 (p) REVERT: B 395 VAL cc_start: 0.8243 (p) cc_final: 0.7872 (t) outliers start: 7 outliers final: 4 residues processed: 153 average time/residue: 0.1745 time to fit residues: 35.7694 Evaluate side-chains 141 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098748 restraints weight = 20596.284| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.69 r_work: 0.3109 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6560 Z= 0.213 Angle : 0.610 8.673 8926 Z= 0.315 Chirality : 0.045 0.233 949 Planarity : 0.005 0.065 1141 Dihedral : 5.625 55.177 988 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.06 % Allowed : 8.41 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 768 helix: 1.41 (0.27), residues: 383 sheet: 0.36 (0.67), residues: 59 loop : -1.15 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 165 HIS 0.008 0.002 HIS A 401 PHE 0.017 0.002 PHE A 369 TYR 0.017 0.002 TYR A 158 ARG 0.010 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 7) link_NAG-ASN : angle 3.22958 ( 21) hydrogen bonds : bond 0.06934 ( 313) hydrogen bonds : angle 4.39029 ( 874) metal coordination : bond 0.00241 ( 2) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.87597 ( 8) covalent geometry : bond 0.00505 ( 6547) covalent geometry : angle 0.58786 ( 8897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.752 Fit side-chains REVERT: A 75 GLU cc_start: 0.7606 (tt0) cc_final: 0.7303 (tt0) REVERT: A 150 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 202 TYR cc_start: 0.8330 (t80) cc_final: 0.7843 (t80) REVERT: A 231 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 243 TYR cc_start: 0.7459 (t80) cc_final: 0.7117 (t80) REVERT: A 299 ASP cc_start: 0.7933 (m-30) cc_final: 0.7698 (m-30) REVERT: A 435 GLU cc_start: 0.7348 (mp0) cc_final: 0.6777 (mp0) REVERT: A 491 VAL cc_start: 0.8438 (t) cc_final: 0.8074 (p) REVERT: A 564 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 395 VAL cc_start: 0.8220 (p) cc_final: 0.7953 (t) outliers start: 14 outliers final: 9 residues processed: 156 average time/residue: 0.2121 time to fit residues: 44.2841 Evaluate side-chains 156 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100296 restraints weight = 21579.299| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.79 r_work: 0.3138 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6560 Z= 0.143 Angle : 0.546 7.386 8926 Z= 0.283 Chirality : 0.042 0.236 949 Planarity : 0.004 0.059 1141 Dihedral : 5.065 55.572 988 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.92 % Allowed : 9.88 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.30), residues: 768 helix: 1.59 (0.27), residues: 380 sheet: 0.49 (0.68), residues: 59 loop : -1.07 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.007 0.001 HIS A 401 PHE 0.013 0.001 PHE A 369 TYR 0.013 0.001 TYR A 158 ARG 0.016 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 7) link_NAG-ASN : angle 2.74128 ( 21) hydrogen bonds : bond 0.05766 ( 313) hydrogen bonds : angle 4.24670 ( 874) metal coordination : bond 0.00090 ( 2) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.70047 ( 8) covalent geometry : bond 0.00321 ( 6547) covalent geometry : angle 0.52823 ( 8897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.649 Fit side-chains REVERT: A 75 GLU cc_start: 0.7587 (tt0) cc_final: 0.7292 (tt0) REVERT: A 202 TYR cc_start: 0.8290 (t80) cc_final: 0.7838 (t80) REVERT: A 243 TYR cc_start: 0.7411 (t80) cc_final: 0.7136 (t80) REVERT: A 299 ASP cc_start: 0.7909 (m-30) cc_final: 0.7676 (m-30) REVERT: A 435 GLU cc_start: 0.7423 (mp0) cc_final: 0.6832 (mp0) REVERT: A 474 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: A 491 VAL cc_start: 0.8405 (t) cc_final: 0.8036 (p) REVERT: A 564 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 395 VAL cc_start: 0.8178 (p) cc_final: 0.7854 (t) REVERT: B 433 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8132 (t) outliers start: 13 outliers final: 6 residues processed: 147 average time/residue: 0.1992 time to fit residues: 38.6083 Evaluate side-chains 144 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.110135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100279 restraints weight = 15388.633| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.25 r_work: 0.3165 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6560 Z= 0.177 Angle : 0.568 7.501 8926 Z= 0.293 Chirality : 0.043 0.250 949 Planarity : 0.004 0.038 1141 Dihedral : 5.022 55.885 988 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.06 % Allowed : 10.03 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 768 helix: 1.55 (0.27), residues: 383 sheet: 0.54 (0.69), residues: 59 loop : -1.01 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.006 0.001 HIS A 401 PHE 0.015 0.001 PHE A 369 TYR 0.015 0.002 TYR B 396 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 7) link_NAG-ASN : angle 2.80932 ( 21) hydrogen bonds : bond 0.06257 ( 313) hydrogen bonds : angle 4.27400 ( 874) metal coordination : bond 0.00087 ( 2) SS BOND : bond 0.00193 ( 4) SS BOND : angle 1.57311 ( 8) covalent geometry : bond 0.00415 ( 6547) covalent geometry : angle 0.54999 ( 8897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.730 Fit side-chains REVERT: A 75 GLU cc_start: 0.7758 (tt0) cc_final: 0.7445 (tt0) REVERT: A 202 TYR cc_start: 0.8356 (t80) cc_final: 0.7858 (t80) REVERT: A 299 ASP cc_start: 0.8037 (m-30) cc_final: 0.7797 (m-30) REVERT: A 435 GLU cc_start: 0.7584 (mp0) cc_final: 0.7001 (mp0) REVERT: A 474 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7271 (mpp) REVERT: A 491 VAL cc_start: 0.8477 (t) cc_final: 0.8108 (p) REVERT: A 564 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 395 VAL cc_start: 0.8248 (p) cc_final: 0.7935 (t) REVERT: B 433 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8228 (t) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.1782 time to fit residues: 36.2808 Evaluate side-chains 155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100215 restraints weight = 22122.224| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.84 r_work: 0.3138 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6560 Z= 0.138 Angle : 0.533 6.911 8926 Z= 0.274 Chirality : 0.042 0.259 949 Planarity : 0.004 0.036 1141 Dihedral : 4.866 55.137 988 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.36 % Allowed : 10.62 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 768 helix: 1.65 (0.27), residues: 380 sheet: 0.52 (0.69), residues: 59 loop : -0.93 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.005 0.001 HIS A 401 PHE 0.013 0.001 PHE A 369 TYR 0.013 0.001 TYR B 396 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 7) link_NAG-ASN : angle 2.55383 ( 21) hydrogen bonds : bond 0.05613 ( 313) hydrogen bonds : angle 4.20529 ( 874) metal coordination : bond 0.00077 ( 2) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.16566 ( 8) covalent geometry : bond 0.00310 ( 6547) covalent geometry : angle 0.51780 ( 8897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7589 (tt0) cc_final: 0.7272 (tt0) REVERT: A 202 TYR cc_start: 0.8283 (t80) cc_final: 0.7821 (t80) REVERT: A 299 ASP cc_start: 0.7917 (m-30) cc_final: 0.7672 (m-30) REVERT: A 474 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: A 491 VAL cc_start: 0.8374 (t) cc_final: 0.8006 (p) REVERT: A 564 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 395 VAL cc_start: 0.8129 (p) cc_final: 0.7738 (t) REVERT: B 433 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8116 (t) outliers start: 16 outliers final: 9 residues processed: 146 average time/residue: 0.1875 time to fit residues: 36.6252 Evaluate side-chains 146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 overall best weight: 0.3362 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.111502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100999 restraints weight = 18611.868| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.53 r_work: 0.3148 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6560 Z= 0.136 Angle : 0.522 6.775 8926 Z= 0.270 Chirality : 0.042 0.263 949 Planarity : 0.004 0.036 1141 Dihedral : 4.748 54.650 988 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.06 % Allowed : 11.06 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 768 helix: 1.68 (0.27), residues: 381 sheet: 0.56 (0.69), residues: 59 loop : -0.85 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 401 PHE 0.012 0.001 PHE A 369 TYR 0.015 0.001 TYR A 587 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 7) link_NAG-ASN : angle 2.49062 ( 21) hydrogen bonds : bond 0.05499 ( 313) hydrogen bonds : angle 4.17571 ( 874) metal coordination : bond 0.00020 ( 2) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.99984 ( 8) covalent geometry : bond 0.00305 ( 6547) covalent geometry : angle 0.50816 ( 8897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7562 (tt0) cc_final: 0.7247 (tt0) REVERT: A 202 TYR cc_start: 0.8266 (t80) cc_final: 0.7866 (t80) REVERT: A 299 ASP cc_start: 0.7937 (m-30) cc_final: 0.7691 (m-30) REVERT: A 474 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: A 475 LYS cc_start: 0.7681 (ptmm) cc_final: 0.7436 (tttm) REVERT: A 491 VAL cc_start: 0.8342 (t) cc_final: 0.7976 (p) REVERT: A 564 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7326 (mm-30) REVERT: B 395 VAL cc_start: 0.8091 (p) cc_final: 0.7708 (t) REVERT: B 433 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8098 (t) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.1787 time to fit residues: 34.3499 Evaluate side-chains 145 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 72 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.111082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100050 restraints weight = 21721.851| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.79 r_work: 0.3127 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6560 Z= 0.149 Angle : 0.541 7.149 8926 Z= 0.279 Chirality : 0.042 0.271 949 Planarity : 0.004 0.036 1141 Dihedral : 4.786 54.730 988 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.06 % Allowed : 11.65 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 768 helix: 1.69 (0.27), residues: 381 sheet: 0.53 (0.68), residues: 59 loop : -0.87 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.015 0.001 TYR A 587 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 2.59642 ( 21) hydrogen bonds : bond 0.05693 ( 313) hydrogen bonds : angle 4.20489 ( 874) metal coordination : bond 0.00034 ( 2) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.00356 ( 8) covalent geometry : bond 0.00341 ( 6547) covalent geometry : angle 0.52634 ( 8897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7598 (tt0) cc_final: 0.7283 (tt0) REVERT: A 202 TYR cc_start: 0.8295 (t80) cc_final: 0.7894 (t80) REVERT: A 299 ASP cc_start: 0.7961 (m-30) cc_final: 0.7716 (m-30) REVERT: A 474 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7179 (mpp) REVERT: A 475 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7470 (tttm) REVERT: A 491 VAL cc_start: 0.8364 (t) cc_final: 0.7996 (p) REVERT: A 564 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 433 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8122 (t) outliers start: 14 outliers final: 10 residues processed: 155 average time/residue: 0.1763 time to fit residues: 36.6869 Evaluate side-chains 152 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 0.2980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.110836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100015 restraints weight = 20118.701| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.70 r_work: 0.3139 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6560 Z= 0.154 Angle : 0.542 6.892 8926 Z= 0.280 Chirality : 0.043 0.274 949 Planarity : 0.004 0.036 1141 Dihedral : 4.797 54.930 988 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 12.24 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 768 helix: 1.67 (0.27), residues: 381 sheet: 0.53 (0.68), residues: 59 loop : -0.83 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR A 587 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 7) link_NAG-ASN : angle 2.56664 ( 21) hydrogen bonds : bond 0.05802 ( 313) hydrogen bonds : angle 4.21282 ( 874) metal coordination : bond 0.00063 ( 2) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.95663 ( 8) covalent geometry : bond 0.00354 ( 6547) covalent geometry : angle 0.52771 ( 8897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7569 (tt0) cc_final: 0.7253 (tt0) REVERT: A 202 TYR cc_start: 0.8287 (t80) cc_final: 0.7871 (t80) REVERT: A 299 ASP cc_start: 0.7937 (m-30) cc_final: 0.7702 (m-30) REVERT: A 424 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 474 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: A 475 LYS cc_start: 0.7691 (ptmm) cc_final: 0.7446 (tttp) REVERT: A 491 VAL cc_start: 0.8357 (t) cc_final: 0.7985 (p) REVERT: B 433 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (t) outliers start: 16 outliers final: 10 residues processed: 155 average time/residue: 0.1779 time to fit residues: 36.7514 Evaluate side-chains 152 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 73 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 17 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.1210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102640 restraints weight = 26047.807| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.15 r_work: 0.3153 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6560 Z= 0.104 Angle : 0.492 5.984 8926 Z= 0.255 Chirality : 0.041 0.266 949 Planarity : 0.004 0.034 1141 Dihedral : 4.519 53.884 988 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 13.27 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.31), residues: 768 helix: 1.85 (0.27), residues: 380 sheet: 0.59 (0.69), residues: 59 loop : -0.67 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 401 PHE 0.019 0.001 PHE A 285 TYR 0.014 0.001 TYR A 587 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 7) link_NAG-ASN : angle 2.10991 ( 21) hydrogen bonds : bond 0.04492 ( 313) hydrogen bonds : angle 4.09691 ( 874) metal coordination : bond 0.00115 ( 2) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.69181 ( 8) covalent geometry : bond 0.00213 ( 6547) covalent geometry : angle 0.48196 ( 8897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7580 (tt0) cc_final: 0.7264 (tt0) REVERT: A 202 TYR cc_start: 0.8244 (t80) cc_final: 0.7895 (t80) REVERT: A 299 ASP cc_start: 0.7944 (m-30) cc_final: 0.7709 (m-30) REVERT: A 360 MET cc_start: 0.7615 (ttp) cc_final: 0.7153 (ptm) REVERT: A 474 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7102 (mpp) REVERT: A 491 VAL cc_start: 0.8298 (t) cc_final: 0.7919 (p) REVERT: A 564 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7261 (mm-30) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.1763 time to fit residues: 32.8977 Evaluate side-chains 140 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 46 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.111088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099782 restraints weight = 22628.080| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.92 r_work: 0.3119 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6560 Z= 0.163 Angle : 0.547 6.660 8926 Z= 0.283 Chirality : 0.043 0.276 949 Planarity : 0.004 0.036 1141 Dihedral : 4.675 54.480 988 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 13.57 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 768 helix: 1.80 (0.27), residues: 381 sheet: 0.63 (0.68), residues: 59 loop : -0.71 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 PHE 0.026 0.002 PHE A 285 TYR 0.015 0.002 TYR B 421 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 2.50522 ( 21) hydrogen bonds : bond 0.05807 ( 313) hydrogen bonds : angle 4.16558 ( 874) metal coordination : bond 0.00195 ( 2) SS BOND : bond 0.00126 ( 4) SS BOND : angle 1.07168 ( 8) covalent geometry : bond 0.00379 ( 6547) covalent geometry : angle 0.53278 ( 8897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4728.38 seconds wall clock time: 84 minutes 24.93 seconds (5064.93 seconds total)