Starting phenix.real_space_refine on Wed Feb 4 04:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sgs_54879/02_2026/9sgs_54879.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 32 5.16 5 C 5505 2.51 5 N 1484 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4317 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 539} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Conformer: "B" Number of residues, atoms: 570, 4317 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 539} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 bond proxies already assigned to first conformer: 4413 Chain: "B" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4316 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 29, 'TRANS': 534} Chain breaks: 5 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 3.08, per 1000 atoms: 0.36 Number of scatterers: 8640 At special positions: 0 Unit cell: (104.648, 98.056, 83.224, 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 32 16.00 O 1619 8.00 N 1484 7.00 C 5505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 562.2 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 58.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.748A pdb=" N HIS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.718A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.697A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 379 through 386 removed outlier: 3.676A pdb=" N LEU A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.761A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.519A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.738A pdb=" N SER A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.059A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.550A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 3.861A pdb=" N LYS A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 593 through 596 Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 634 removed outlier: 3.582A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 692 through 701 removed outlier: 4.206A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.672A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 154 through 159 removed outlier: 7.529A pdb=" N LYS B 157 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.653A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.752A pdb=" N ILE B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.874A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.650A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.602A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.850A pdb=" N ARG B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.921A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.644A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 531 Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 580 through 586 removed outlier: 4.339A pdb=" N VAL B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 596 Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 634 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 692 through 698 removed outlier: 3.847A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.519A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA6, first strand: chain 'B' and resid 667 through 670 423 hydrogen bonds defined for protein. 1160 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: 1.37 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2873 1.34 - 1.46: 2099 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 8850 Sorted by residual: bond pdb=" CB ASP A 240 " pdb=" CG ASP A 240 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CG LEU A 48 " pdb=" CD1 LEU A 48 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB ASP B 612 " pdb=" CG ASP B 612 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB PRO A 388 " pdb=" CG PRO A 388 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.48e-01 bond pdb=" C ASN A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.326 1.340 -0.014 1.44e-02 4.82e+03 9.32e-01 ... (remaining 8845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 11970 2.98 - 5.95: 66 5.95 - 8.93: 6 8.93 - 11.91: 3 11.91 - 14.89: 1 Bond angle restraints: 12046 Sorted by residual: angle pdb=" N ALA B 453 " pdb=" CA ALA B 453 " pdb=" C ALA B 453 " ideal model delta sigma weight residual 114.75 108.60 6.15 1.26e+00 6.30e-01 2.38e+01 angle pdb=" CA LEU A 378 " pdb=" CB LEU A 378 " pdb=" CG LEU A 378 " ideal model delta sigma weight residual 116.30 131.19 -14.89 3.50e+00 8.16e-02 1.81e+01 angle pdb=" N ASN B 508 " pdb=" CA ASN B 508 " pdb=" C ASN B 508 " ideal model delta sigma weight residual 112.97 109.19 3.78 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C GLY A 512 " pdb=" N ASP A 513 " pdb=" CA ASP A 513 " ideal model delta sigma weight residual 120.82 126.04 -5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" CB MET A 664 " pdb=" CG MET A 664 " pdb=" SD MET A 664 " ideal model delta sigma weight residual 112.70 123.05 -10.35 3.00e+00 1.11e-01 1.19e+01 ... (remaining 12041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4657 17.73 - 35.45: 398 35.45 - 53.18: 86 53.18 - 70.91: 20 70.91 - 88.63: 12 Dihedral angle restraints: 5173 sinusoidal: 1954 harmonic: 3219 Sorted by residual: dihedral pdb=" CA MET A 377 " pdb=" C MET A 377 " pdb=" N LEU A 378 " pdb=" CA LEU A 378 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASN B 508 " pdb=" C ASN B 508 " pdb=" N ASP B 509 " pdb=" CA ASP B 509 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY A 512 " pdb=" C GLY A 512 " pdb=" N ASP A 513 " pdb=" CA ASP A 513 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 5170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 724 0.025 - 0.050: 342 0.050 - 0.075: 175 0.075 - 0.100: 57 0.100 - 0.125: 24 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA PRO A 388 " pdb=" N PRO A 388 " pdb=" C PRO A 388 " pdb=" CB PRO A 388 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ASP B 487 " pdb=" N ASP B 487 " pdb=" C ASP B 487 " pdb=" CB ASP B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 666 " pdb=" N ILE A 666 " pdb=" C ILE A 666 " pdb=" CB ILE A 666 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1319 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 669 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO B 670 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 717 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 718 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 718 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 718 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 604 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 605 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 605 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 605 " 0.026 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1713 2.77 - 3.30: 8415 3.30 - 3.84: 14546 3.84 - 4.37: 16889 4.37 - 4.90: 29255 Nonbonded interactions: 70818 Sorted by model distance: nonbonded pdb=" NH1 ARG A 128 " pdb=" OE2 GLU B 703 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.255 3.040 nonbonded pdb=" O THR A 380 " pdb=" OG SER A 383 " model vdw 2.263 3.040 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.267 3.040 nonbonded pdb=" NH2 ARG B 484 " pdb=" OD2 ASP B 487 " model vdw 2.330 3.120 ... (remaining 70813 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 107 or resid 109 through 126 or resid 140 throu \ gh 191 or resid 239 through 346 or resid 352 through 355 or resid 375 through 64 \ 7 or (resid 648 through 649 and (name N or name CA or name C or name O or name C \ B )) or resid 650 through 739)) selection = (chain 'B' and (resid 41 through 107 or resid 109 through 334 or (resid 335 and \ (name N or name CA or name C or name O or name CB )) or resid 336 through 338 or \ (resid 339 through 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 or (resid 342 and (name N or name CA or name C or name O or name C \ B )) or resid 343 through 344 or (resid 345 and (name N or name CA or name C or \ name O or name CB )) or resid 346 or (resid 352 and (name N or name CA or name C \ or name O or name CB )) or resid 353 through 355 or resid 375 through 398 or (r \ esid 399 and (name N or name CA or name C or name O or name CB )) or resid 400 t \ hrough 518 or (resid 519 and (name N or name CA or name C or name O or name CB ) \ ) or resid 520 through 525 or (resid 526 and (name N or name CA or name C or nam \ e O or name CB )) or resid 527 through 589 or (resid 590 through 591 and (name N \ or name CA or name C or name O or name CB )) or resid 592 through 639 or (resid \ 640 and (name N or name CA or name C or name O or name CB )) or resid 641 throu \ gh 650 or (resid 651 and (name N or name CA or name C or name O or name CB )) or \ resid 652 through 739)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8850 Z= 0.127 Angle : 0.614 14.887 12046 Z= 0.319 Chirality : 0.039 0.125 1322 Planarity : 0.006 0.059 1569 Dihedral : 14.745 88.632 3107 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.58 % Allowed : 17.51 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1111 helix: 0.89 (0.22), residues: 576 sheet: -1.33 (1.15), residues: 18 loop : -1.25 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 396 TYR 0.011 0.001 TYR A 638 PHE 0.008 0.001 PHE A 720 TRP 0.022 0.001 TRP A 341 HIS 0.013 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8850) covalent geometry : angle 0.61430 (12046) hydrogen bonds : bond 0.15969 ( 423) hydrogen bonds : angle 5.03681 ( 1160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.396 Fit side-chains REVERT: B 702 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8205 (p) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.5845 time to fit residues: 24.1424 Evaluate side-chains 34 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain B residue 702 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.067629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051248 restraints weight = 31809.421| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.99 r_work: 0.2566 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8850 Z= 0.110 Angle : 0.537 12.544 12046 Z= 0.275 Chirality : 0.039 0.138 1322 Planarity : 0.005 0.048 1569 Dihedral : 4.215 49.226 1214 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 1.15 % Allowed : 14.75 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1111 helix: 1.21 (0.22), residues: 582 sheet: -2.35 (2.22), residues: 8 loop : -1.01 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 396 TYR 0.015 0.001 TYR B 64 PHE 0.008 0.001 PHE A 720 TRP 0.013 0.001 TRP A 341 HIS 0.013 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8850) covalent geometry : angle 0.53703 (12046) hydrogen bonds : bond 0.03891 ( 423) hydrogen bonds : angle 4.15427 ( 1160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.309 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 39 average time/residue: 0.5814 time to fit residues: 24.5555 Evaluate side-chains 32 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN B 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.049324 restraints weight = 38719.259| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 4.32 r_work: 0.2511 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8850 Z= 0.143 Angle : 0.519 10.220 12046 Z= 0.261 Chirality : 0.039 0.139 1322 Planarity : 0.004 0.044 1569 Dihedral : 3.980 42.370 1212 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 0.69 % Allowed : 14.86 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1111 helix: 1.33 (0.22), residues: 585 sheet: -0.26 (1.25), residues: 18 loop : -0.87 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.017 0.001 TYR A 155 PHE 0.010 0.001 PHE A 720 TRP 0.007 0.001 TRP A 149 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8850) covalent geometry : angle 0.51883 (12046) hydrogen bonds : bond 0.03820 ( 423) hydrogen bonds : angle 3.92972 ( 1160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.344 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 35 average time/residue: 0.6523 time to fit residues: 24.5859 Evaluate side-chains 31 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049170 restraints weight = 38987.556| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 4.33 r_work: 0.2502 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8850 Z= 0.142 Angle : 0.511 12.842 12046 Z= 0.254 Chirality : 0.039 0.139 1322 Planarity : 0.004 0.043 1569 Dihedral : 3.628 21.503 1210 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 0.81 % Allowed : 14.75 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1111 helix: 1.49 (0.22), residues: 580 sheet: -0.00 (1.26), residues: 18 loop : -0.80 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.016 0.001 TYR A 155 PHE 0.010 0.001 PHE A 720 TRP 0.006 0.001 TRP A 149 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8850) covalent geometry : angle 0.51137 (12046) hydrogen bonds : bond 0.03529 ( 423) hydrogen bonds : angle 3.82130 ( 1160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.349 Fit side-chains REVERT: A 377 MET cc_start: 0.8373 (mtm) cc_final: 0.7871 (ppp) outliers start: 7 outliers final: 1 residues processed: 36 average time/residue: 0.5951 time to fit residues: 23.1619 Evaluate side-chains 31 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 111 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052038 restraints weight = 28472.317| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.81 r_work: 0.2570 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8850 Z= 0.088 Angle : 0.495 12.493 12046 Z= 0.240 Chirality : 0.038 0.139 1322 Planarity : 0.004 0.040 1569 Dihedral : 3.468 22.810 1210 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 0.58 % Allowed : 15.55 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1111 helix: 1.64 (0.22), residues: 581 sheet: 0.75 (0.98), residues: 28 loop : -0.76 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE A 483 TRP 0.005 0.001 TRP A 149 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8850) covalent geometry : angle 0.49530 (12046) hydrogen bonds : bond 0.03038 ( 423) hydrogen bonds : angle 3.73024 ( 1160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.373 Fit side-chains REVERT: A 377 MET cc_start: 0.8322 (mtm) cc_final: 0.7989 (ppp) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.6012 time to fit residues: 24.1072 Evaluate side-chains 32 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047439 restraints weight = 49988.083| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 4.82 r_work: 0.2444 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8850 Z= 0.212 Angle : 0.552 12.118 12046 Z= 0.273 Chirality : 0.040 0.138 1322 Planarity : 0.004 0.047 1569 Dihedral : 3.638 23.249 1210 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.04 % Allowed : 15.21 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1111 helix: 1.64 (0.22), residues: 580 sheet: 0.02 (1.25), residues: 18 loop : -0.69 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.020 0.001 TYR A 155 PHE 0.012 0.002 PHE A 720 TRP 0.008 0.001 TRP A 91 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8850) covalent geometry : angle 0.55165 (12046) hydrogen bonds : bond 0.03879 ( 423) hydrogen bonds : angle 3.80515 ( 1160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.342 Fit side-chains REVERT: A 377 MET cc_start: 0.8551 (mtm) cc_final: 0.7842 (ppp) REVERT: B 609 MET cc_start: 0.8909 (mmp) cc_final: 0.8700 (mmp) outliers start: 9 outliers final: 2 residues processed: 36 average time/residue: 0.5877 time to fit residues: 22.9979 Evaluate side-chains 32 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 103 optimal weight: 0.0030 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051147 restraints weight = 23458.469| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.42 r_work: 0.2576 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8850 Z= 0.097 Angle : 0.486 11.715 12046 Z= 0.239 Chirality : 0.038 0.136 1322 Planarity : 0.004 0.044 1569 Dihedral : 3.496 23.050 1210 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.69 % Allowed : 15.44 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1111 helix: 1.72 (0.22), residues: 581 sheet: 0.12 (1.23), residues: 18 loop : -0.67 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.013 0.001 TYR A 155 PHE 0.008 0.001 PHE A 720 TRP 0.006 0.001 TRP B 477 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8850) covalent geometry : angle 0.48552 (12046) hydrogen bonds : bond 0.03147 ( 423) hydrogen bonds : angle 3.70924 ( 1160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.372 Fit side-chains REVERT: A 242 MET cc_start: 0.9157 (mmm) cc_final: 0.8864 (mmm) REVERT: A 377 MET cc_start: 0.8409 (mtm) cc_final: 0.7926 (ppp) REVERT: B 596 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8096 (m-40) outliers start: 6 outliers final: 1 residues processed: 36 average time/residue: 0.5911 time to fit residues: 23.0510 Evaluate side-chains 32 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.050639 restraints weight = 28273.097| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.80 r_work: 0.2546 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8850 Z= 0.114 Angle : 0.514 11.403 12046 Z= 0.248 Chirality : 0.039 0.154 1322 Planarity : 0.004 0.043 1569 Dihedral : 3.450 22.759 1210 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.81 % Allowed : 15.44 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1111 helix: 1.76 (0.22), residues: 581 sheet: 0.15 (1.23), residues: 18 loop : -0.67 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.015 0.001 TYR A 155 PHE 0.009 0.001 PHE A 720 TRP 0.006 0.001 TRP B 477 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8850) covalent geometry : angle 0.51443 (12046) hydrogen bonds : bond 0.03205 ( 423) hydrogen bonds : angle 3.66875 ( 1160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.368 Fit side-chains REVERT: A 242 MET cc_start: 0.9152 (mmm) cc_final: 0.8877 (mmm) REVERT: A 377 MET cc_start: 0.8436 (mtm) cc_final: 0.7918 (ppp) REVERT: B 596 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8043 (m-40) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.5979 time to fit residues: 23.9973 Evaluate side-chains 35 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 93 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.049203 restraints weight = 23600.051| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.39 r_work: 0.2521 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8850 Z= 0.212 Angle : 0.554 11.247 12046 Z= 0.271 Chirality : 0.040 0.153 1322 Planarity : 0.004 0.047 1569 Dihedral : 3.576 22.951 1210 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.81 % Allowed : 15.21 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1111 helix: 1.76 (0.22), residues: 578 sheet: 0.27 (1.27), residues: 18 loop : -0.70 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.019 0.001 TYR A 155 PHE 0.011 0.001 PHE A 720 TRP 0.008 0.001 TRP A 91 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8850) covalent geometry : angle 0.55442 (12046) hydrogen bonds : bond 0.03680 ( 423) hydrogen bonds : angle 3.73823 ( 1160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.377 Fit side-chains REVERT: A 242 MET cc_start: 0.9151 (mmm) cc_final: 0.8872 (mmm) REVERT: A 377 MET cc_start: 0.8467 (mtm) cc_final: 0.7861 (ppp) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.5962 time to fit residues: 23.2569 Evaluate side-chains 35 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.049969 restraints weight = 41807.996| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.53 r_work: 0.2511 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8850 Z= 0.098 Angle : 0.517 11.456 12046 Z= 0.248 Chirality : 0.038 0.147 1322 Planarity : 0.004 0.044 1569 Dihedral : 3.441 22.914 1210 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.46 % Allowed : 15.67 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1111 helix: 1.77 (0.22), residues: 578 sheet: 0.14 (1.24), residues: 18 loop : -0.65 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.013 0.001 TYR A 155 PHE 0.008 0.001 PHE A 720 TRP 0.006 0.001 TRP B 477 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8850) covalent geometry : angle 0.51721 (12046) hydrogen bonds : bond 0.03106 ( 423) hydrogen bonds : angle 3.66673 ( 1160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.333 Fit side-chains REVERT: A 242 MET cc_start: 0.9163 (mmm) cc_final: 0.8883 (mmm) REVERT: A 377 MET cc_start: 0.8488 (mtm) cc_final: 0.7877 (ppp) REVERT: B 126 MET cc_start: 0.7122 (tpp) cc_final: 0.6918 (tpp) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.6468 time to fit residues: 23.6775 Evaluate side-chains 34 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.0050 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.051887 restraints weight = 23233.004| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.42 r_work: 0.2593 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8850 Z= 0.096 Angle : 0.501 12.751 12046 Z= 0.240 Chirality : 0.038 0.145 1322 Planarity : 0.004 0.043 1569 Dihedral : 3.302 22.180 1210 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.58 % Allowed : 15.44 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1111 helix: 1.85 (0.22), residues: 581 sheet: 0.18 (1.25), residues: 18 loop : -0.59 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.014 0.001 TYR A 155 PHE 0.008 0.001 PHE A 720 TRP 0.006 0.001 TRP B 149 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8850) covalent geometry : angle 0.50141 (12046) hydrogen bonds : bond 0.02962 ( 423) hydrogen bonds : angle 3.59288 ( 1160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.83 seconds wall clock time: 48 minutes 21.73 seconds (2901.73 seconds total)