Starting phenix.real_space_refine on Fri Sep 11 07:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.map" model { file = "/net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a8z_11680/09_2026/7a8z_11680.cif" } resolution = 3.35 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= 0.036 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 28 5.16 5 C 5352 2.51 5 N 1447 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8402 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4211 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 29, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4191 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 521} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 1.99, per 1000 atoms: 0.24 Number of scatterers: 8402 At special positions: 0 Unit cell: (99.75, 126, 82.95, 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 28 16.00 O 1575 8.00 N 1447 7.00 C 5352 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: 0.60 Conformation dependent library (CDL) restraints added in 379.8 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 55.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.650A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.614A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (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 175 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.877A pdb=" N ALA A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.164A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.540A pdb=" N ARG A 392 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.675A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.732A pdb=" N ASP A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.693A pdb=" N ARG A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.713A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.521A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.542A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.536A pdb=" N THR A 579 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 620 through 635 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 692 through 701 Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.759A pdb=" N PHE A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 738' Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.849A pdb=" N GLU B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.525A pdb=" N THR B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.212A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 4.564A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.942A pdb=" N ILE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.017A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 4.146A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.773A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.520A pdb=" N TYR B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.683A pdb=" N ASP B 440 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.679A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.990A pdb=" N ASP B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 514' Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.744A pdb=" N SER B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 605 through 617 removed outlier: 3.824A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 694 through 698 removed outlier: 3.959A pdb=" N VAL B 697 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 Processing helix chain 'B' and resid 734 through 736 No H-bonds generated for 'chain 'B' and resid 734 through 736' Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 668 removed outlier: 6.918A pdb=" N GLY A 680 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA4, first strand: chain 'B' and resid 666 through 668 removed outlier: 6.509A pdb=" N ASP B 682 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 687 " --> pdb=" O ASP B 682 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1005 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: 1.16 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2795 1.34 - 1.46: 1444 1.46 - 1.58: 4310 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 8601 Sorted by residual: bond pdb=" CG PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 1.503 1.561 -0.058 3.40e-02 8.65e+02 2.95e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.37e+00 bond pdb=" CB VAL B 166 " pdb=" CG1 VAL B 166 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CA ASP B 513 " pdb=" CB ASP B 513 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.67e-02 3.59e+03 9.16e-01 ... (remaining 8596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11446 1.61 - 3.22: 217 3.22 - 4.83: 32 4.83 - 6.44: 12 6.44 - 8.06: 1 Bond angle restraints: 11708 Sorted by residual: angle pdb=" N ARG A 515 " pdb=" CA ARG A 515 " pdb=" C ARG A 515 " ideal model delta sigma weight residual 113.12 108.62 4.50 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C PRO A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 121.65 118.27 3.38 9.40e-01 1.13e+00 1.29e+01 angle pdb=" N VAL B 710 " pdb=" CA VAL B 710 " pdb=" C VAL B 710 " ideal model delta sigma weight residual 111.81 108.81 3.00 8.60e-01 1.35e+00 1.21e+01 angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 107.81 4.19 1.40e+00 5.10e-01 8.97e+00 angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 106.21 109.33 -3.12 1.07e+00 8.73e-01 8.51e+00 ... (remaining 11703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4480 17.14 - 34.27: 442 34.27 - 51.40: 89 51.40 - 68.54: 22 68.54 - 85.67: 6 Dihedral angle restraints: 5039 sinusoidal: 1912 harmonic: 3127 Sorted by residual: dihedral pdb=" CA VAL A 423 " pdb=" C VAL A 423 " pdb=" N ALA A 424 " pdb=" CA ALA A 424 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 513 " pdb=" C ASP A 513 " pdb=" N LEU A 514 " pdb=" CA LEU A 514 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU A 604 " pdb=" C LEU A 604 " pdb=" N PRO A 605 " pdb=" CA PRO A 605 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 667 0.027 - 0.055: 398 0.055 - 0.082: 158 0.082 - 0.110: 55 0.110 - 0.137: 11 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA PRO A 605 " pdb=" N PRO A 605 " pdb=" C PRO A 605 " pdb=" CB PRO A 605 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ASN B 330 " pdb=" N ASN B 330 " pdb=" C ASN B 330 " pdb=" CB ASN B 330 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1286 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 91 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 92 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 99 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 100 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 604 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 605 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 605 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 605 " 0.021 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2003 2.78 - 3.31: 7835 3.31 - 3.84: 13189 3.84 - 4.37: 15440 4.37 - 4.90: 27330 Nonbonded interactions: 65797 Sorted by model distance: nonbonded pdb=" O GLU B 67 " pdb=" OG1 THR B 70 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP A 580 " pdb=" OG SER A 583 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN B 88 " pdb=" NE1 TRP B 90 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASP A 592 " pdb=" NZ LYS A 613 " model vdw 2.305 3.120 nonbonded pdb=" O GLU A 67 " pdb=" OG1 THR A 70 " model vdw 2.314 3.040 ... (remaining 65792 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 42 through 124 or resid 141 through 190 or resid 238 throu \ gh 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 251 through 384 or (resid 385 and (name N or name CA or name C or name O \ or name CB )) or resid 386 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or resid 408 through 4 \ 62 or (resid 463 through 464 and (name N or name CA or name C or name O or name \ CB )) or resid 465 through 525 or (resid 526 and (name N or name CA or name C or \ name O or name CB )) or resid 527 through 639 or (resid 640 and (name N or name \ CA or name C or name O or name CB )) or resid 641 through 739 or (resid 740 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 42 through 142 or (resid 143 through 144 and (name N or na \ me CA or name C or name O or name CB )) or resid 145 through 152 or (resid 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 271 \ or resid 329 through 344 or (resid 345 and (name N or name CA or name C or name \ O or name CB )) or resid 378 through 391 or (resid 392 and (name N or name CA o \ r name C or name O or name CB )) or resid 393 through 398 or (resid 399 and (nam \ e N or name CA or name C or name O or name CB )) or resid 400 through 486 or (re \ sid 487 and (name N or name CA or name C or name O or name CB )) or resid 488 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 or (resid 515 and (name N or name CA or name C or name O or name C \ B )) or resid 516 through 556 or (resid 557 through 559 and (name N or name CA o \ r name C or name O or name CB )) or resid 560 through 647 or (resid 648 through \ 649 and (name N or name CA or name C or name O or name CB )) or resid 650 throug \ h 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) or \ resid 687 through 740)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.004 0.060 8601 Z= 0.166 Angle : 0.588 8.055 11708 Z= 0.326 Chirality : 0.041 0.137 1289 Planarity : 0.005 0.112 1531 Dihedral : 14.415 85.674 3033 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.49 (0.25), residues: 1083 helix: -0.10 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 395 TYR 0.009 0.001 TYR A 597 PHE 0.011 0.001 PHE A 332 TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8601) covalent geometry : angle 0.58775 / 0.33 (11708) hydrogen bonds : bond 0.17418 / 11.95 ( 356) hydrogen bonds : angle 6.04200 / 4.25 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.233 Fit side-chains REVERT: B 557 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7242 (ttmt) REVERT: B 723 ASP cc_start: 0.7724 (t70) cc_final: 0.7418 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1119 time to fit residues: 12.7295 Evaluate side-chains 70 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109972 restraints weight = 10820.373| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.17 r_work: 0.3163 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8601 Z= 0.117 Angle : 0.528 5.661 11708 Z= 0.271 Chirality : 0.040 0.147 1289 Planarity : 0.005 0.070 1531 Dihedral : 4.314 23.396 1178 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.02 % Favored : 92.89 % Rotamer: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.14 % 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: -1.03 (0.25), residues: 1083 helix: 0.42 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 484 TYR 0.010 0.001 TYR B 337 PHE 0.011 0.001 PHE A 332 TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8601) covalent geometry : angle 0.52774 / 0.27 (11708) hydrogen bonds : bond 0.03848 / 2.50 ( 356) hydrogen bonds : angle 4.11246 / 2.90 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.317 Fit side-chains REVERT: B 155 TYR cc_start: 0.8760 (m-80) cc_final: 0.8145 (m-80) REVERT: B 626 VAL cc_start: 0.7976 (t) cc_final: 0.7746 (p) outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.1017 time to fit residues: 11.7891 Evaluate side-chains 72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 337 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106586 restraints weight = 10838.309| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.99 r_work: 0.3126 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8601 Z= 0.173 Angle : 0.549 5.541 11708 Z= 0.280 Chirality : 0.041 0.159 1289 Planarity : 0.004 0.060 1531 Dihedral : 4.330 24.266 1178 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.94 % Favored : 91.97 % Rotamer: Outliers : 0.83 % Allowed : 9.69 % Favored : 89.48 % 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: -1.00 (0.25), residues: 1083 helix: 0.46 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 484 TYR 0.011 0.002 TYR B 638 PHE 0.011 0.001 PHE A 62 TRP 0.009 0.001 TRP A 191 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 8601) covalent geometry : angle 0.54939 / 0.28 (11708) hydrogen bonds : bond 0.04055 / 2.61 ( 356) hydrogen bonds : angle 3.96516 / 2.82 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.310 Fit side-chains REVERT: A 514 LEU cc_start: 0.7639 (tp) cc_final: 0.7240 (tp) REVERT: B 608 TYR cc_start: 0.7987 (m-80) cc_final: 0.7676 (m-80) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.1045 time to fit residues: 11.1860 Evaluate side-chains 73 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107145 restraints weight = 11074.061| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.06 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8601 Z= 0.131 Angle : 0.517 6.048 11708 Z= 0.262 Chirality : 0.040 0.151 1289 Planarity : 0.004 0.052 1531 Dihedral : 4.139 23.194 1178 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 0.95 % Allowed : 11.35 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.26), residues: 1083 helix: 0.66 (0.24), residues: 530 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 484 TYR 0.010 0.001 TYR A 337 PHE 0.011 0.001 PHE A 62 TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8601) covalent geometry : angle 0.51681 / 0.26 (11708) hydrogen bonds : bond 0.03559 / 2.29 ( 356) hydrogen bonds : angle 3.80763 / 2.69 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.342 Fit side-chains REVERT: A 407 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: A 437 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8905 (tt) REVERT: B 608 TYR cc_start: 0.7924 (m-80) cc_final: 0.7581 (m-80) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.1126 time to fit residues: 12.8837 Evaluate side-chains 76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106926 restraints weight = 10982.526| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.02 r_work: 0.3133 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8601 Z= 0.190 Angle : 0.556 5.559 11708 Z= 0.281 Chirality : 0.041 0.165 1289 Planarity : 0.004 0.051 1531 Dihedral : 4.237 23.900 1178 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 1.06 % Allowed : 12.88 % Favored : 86.05 % 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: -0.91 (0.25), residues: 1083 helix: 0.57 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.010 0.002 TYR B 638 PHE 0.010 0.001 PHE A 62 TRP 0.009 0.001 TRP A 191 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 8601) covalent geometry : angle 0.55620 / 0.28 (11708) hydrogen bonds : bond 0.03963 / 2.54 ( 356) hydrogen bonds : angle 3.86630 / 2.74 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.257 Fit side-chains REVERT: A 407 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: A 437 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 420 MET cc_start: 0.8951 (ttt) cc_final: 0.8336 (ttt) REVERT: B 608 TYR cc_start: 0.8006 (m-80) cc_final: 0.7661 (m-80) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.0925 time to fit residues: 10.1459 Evaluate side-chains 75 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108592 restraints weight = 10862.426| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.16 r_work: 0.3160 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8601 Z= 0.118 Angle : 0.515 6.654 11708 Z= 0.260 Chirality : 0.039 0.161 1289 Planarity : 0.004 0.047 1531 Dihedral : 4.005 25.148 1178 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 1.30 % Allowed : 13.24 % Favored : 85.46 % 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: -0.71 (0.26), residues: 1083 helix: 0.78 (0.24), residues: 530 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.011 0.001 TYR A 337 PHE 0.011 0.001 PHE A 62 TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8601) covalent geometry : angle 0.51486 / 0.26 (11708) hydrogen bonds : bond 0.03371 / 2.17 ( 356) hydrogen bonds : angle 3.71066 / 2.62 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 407 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 437 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 608 TYR cc_start: 0.8012 (m-80) cc_final: 0.7646 (m-80) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.1060 time to fit residues: 11.6526 Evaluate side-chains 76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117838 restraints weight = 11690.604| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.05 r_work: 0.3296 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8601 Z= 0.127 Angle : 0.517 5.724 11708 Z= 0.261 Chirality : 0.040 0.171 1289 Planarity : 0.004 0.046 1531 Dihedral : 3.948 24.136 1178 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.94 % Favored : 91.97 % Rotamer: Outliers : 1.30 % Allowed : 13.24 % Favored : 85.46 % 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: -0.61 (0.26), residues: 1083 helix: 0.87 (0.24), residues: 530 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.011 0.001 TYR A 337 PHE 0.011 0.001 PHE B 102 TRP 0.008 0.001 TRP A 191 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8601) covalent geometry : angle 0.51682 / 0.26 (11708) hydrogen bonds : bond 0.03400 / 2.19 ( 356) hydrogen bonds : angle 3.65591 / 2.58 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.306 Fit side-chains REVERT: A 407 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 420 MET cc_start: 0.8823 (ttt) cc_final: 0.8446 (ttt) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.1034 time to fit residues: 11.3013 Evaluate side-chains 76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 41 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.0419 > 50:) chunk 107 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118102 restraints weight = 11518.347| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.04 r_work: 0.3299 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8601 Z= 0.130 Angle : 0.522 7.929 11708 Z= 0.262 Chirality : 0.040 0.171 1289 Planarity : 0.004 0.045 1531 Dihedral : 3.934 23.219 1178 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.02 % Favored : 92.89 % Rotamer: Outliers : 1.18 % Allowed : 13.83 % Favored : 84.99 % 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: -0.58 (0.26), residues: 1083 helix: 0.90 (0.24), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.011 0.001 TYR A 337 PHE 0.009 0.001 PHE A 62 TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8601) covalent geometry : angle 0.52202 / 0.26 (11708) hydrogen bonds : bond 0.03388 / 2.17 ( 356) hydrogen bonds : angle 3.63282 / 2.56 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.302 Fit side-chains REVERT: A 407 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 732 MET cc_start: 0.8290 (mmp) cc_final: 0.8008 (mmp) REVERT: B 420 MET cc_start: 0.8882 (ttt) cc_final: 0.8420 (ttt) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.1052 time to fit residues: 11.2933 Evaluate side-chains 79 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120037 restraints weight = 11516.639| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.02 r_work: 0.3325 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8601 Z= 0.107 Angle : 0.503 7.035 11708 Z= 0.254 Chirality : 0.039 0.172 1289 Planarity : 0.004 0.044 1531 Dihedral : 3.782 23.583 1178 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % Rotamer: Outliers : 1.18 % Allowed : 14.18 % Favored : 84.63 % 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: -0.42 (0.26), residues: 1083 helix: 1.04 (0.24), residues: 531 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.012 0.001 TYR B 678 PHE 0.008 0.001 PHE A 62 TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8601) covalent geometry : angle 0.50342 / 0.25 (11708) hydrogen bonds : bond 0.03083 / 1.98 ( 356) hydrogen bonds : angle 3.54191 / 2.50 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.322 Fit side-chains REVERT: A 407 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 420 MET cc_start: 0.8748 (ttt) cc_final: 0.8510 (ttt) REVERT: B 155 TYR cc_start: 0.8923 (m-80) cc_final: 0.8436 (m-80) REVERT: B 420 MET cc_start: 0.8860 (ttt) cc_final: 0.8371 (ttt) REVERT: B 535 ASN cc_start: 0.8104 (t0) cc_final: 0.7865 (t0) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1034 time to fit residues: 11.7514 Evaluate side-chains 81 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119548 restraints weight = 11407.762| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.00 r_work: 0.3322 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8601 Z= 0.113 Angle : 0.507 6.987 11708 Z= 0.254 Chirality : 0.040 0.170 1289 Planarity : 0.004 0.045 1531 Dihedral : 3.763 23.076 1178 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 0.95 % Allowed : 14.42 % Favored : 84.63 % 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: -0.38 (0.26), residues: 1083 helix: 1.10 (0.24), residues: 531 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.011 0.001 TYR B 678 PHE 0.008 0.001 PHE A 62 TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 8601) covalent geometry : angle 0.50687 / 0.25 (11708) hydrogen bonds : bond 0.03182 / 2.04 ( 356) hydrogen bonds : angle 3.51155 / 2.48 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.316 Fit side-chains REVERT: A 407 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 420 MET cc_start: 0.8824 (ttt) cc_final: 0.8548 (ttt) REVERT: A 732 MET cc_start: 0.8299 (mmp) cc_final: 0.7992 (mmp) REVERT: B 155 TYR cc_start: 0.8925 (m-80) cc_final: 0.8430 (m-80) REVERT: B 420 MET cc_start: 0.8851 (ttt) cc_final: 0.8350 (ttt) REVERT: B 535 ASN cc_start: 0.8103 (t0) cc_final: 0.7869 (t0) REVERT: B 608 TYR cc_start: 0.8386 (m-80) cc_final: 0.8096 (m-80) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.1091 time to fit residues: 12.7035 Evaluate side-chains 83 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 101 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118952 restraints weight = 11524.210| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.01 r_work: 0.3314 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.003 0.028 8601 Z= 0.125 Angle : 0.517 6.787 11708 Z= 0.258 Chirality : 0.040 0.170 1289 Planarity : 0.004 0.046 1531 Dihedral : 3.801 22.493 1178 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 1.42 % Allowed : 14.18 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.48 (0.26), residues: 1083 helix: 1.02 (0.24), residues: 536 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.011 0.001 TYR B 678 PHE 0.008 0.001 PHE A 62 TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8601) covalent geometry : angle 0.51735 / 0.26 (11708) hydrogen bonds : bond 0.03294 / 2.11 ( 356) hydrogen bonds : angle 3.52800 / 2.49 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.52 seconds wall clock time: 31 minutes 6.16 seconds (1866.16 seconds total)