Starting phenix.real_space_refine on Wed Mar 4 02:43:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.map" model { file = "/net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a7a_11676/03_2026/7a7a_11676.cif" } resolution = 3.08 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 34 5.16 5 C 6450 2.51 5 N 1739 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5000 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 40, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5061 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 43, 'TRANS': 623} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10147 At special positions: 0 Unit cell: (84.76, 95.192, 125.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 34 16.00 O 1922 8.00 N 1739 7.00 C 6450 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 486.6 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 50.8% alpha, 1.6% 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 44 through 48 removed outlier: 3.560A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.553A pdb=" N GLU A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.001A pdb=" N SER A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.181A pdb=" N ARG A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.487A 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 175 Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.525A pdb=" N VAL A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.807A pdb=" N ARG A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.595A 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 removed outlier: 3.529A pdb=" N ASP A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 3.936A 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: 3.534A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.675A pdb=" N ARG A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.787A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 588 removed outlier: 3.629A pdb=" N PHE A 584 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 585 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 634 removed outlier: 4.033A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.974A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 removed outlier: 3.536A pdb=" N VAL A 721 " --> pdb=" O GLN A 717 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.800A pdb=" N GLU B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.652A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.666A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.583A 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 176 removed outlier: 3.563A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.035A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.636A pdb=" N MET B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.761A pdb=" N ILE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.538A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.704A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.838A 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 451 through 464 removed outlier: 3.510A pdb=" N ALA B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.875A 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: 3.810A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 removed outlier: 3.910A pdb=" N ILE B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.798A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.719A pdb=" N ALA B 585 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 586' Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 634 removed outlier: 3.747A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 693 through 701 removed outlier: 4.412A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 4.178A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 733 Processing sheet with id=AA1, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA2, first strand: chain 'B' and resid 667 through 670 removed outlier: 6.132A pdb=" N TYR B 678 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 690 " --> pdb=" O TYR B 678 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 680 " --> pdb=" O LYS B 688 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1026 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: 1.56 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 4260 1.39 - 1.55: 6092 1.55 - 1.72: 1 1.72 - 1.88: 64 1.88 - 2.05: 8 Bond restraints: 10425 Sorted by residual: bond pdb=" CB TRP B 397 " pdb=" CG TRP B 397 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.37e+00 bond pdb=" CG LEU B 298 " pdb=" CD1 LEU B 298 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" CB ASN B 655 " pdb=" CG ASN B 655 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CG LEU B 141 " pdb=" CD1 LEU B 141 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CG LEU A 543 " pdb=" CD1 LEU A 543 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 ... (remaining 10420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 13746 1.76 - 3.52: 421 3.52 - 5.28: 58 5.28 - 7.04: 12 7.04 - 8.80: 7 Bond angle restraints: 14244 Sorted by residual: angle pdb=" C THR A 275 " pdb=" N HIS A 276 " pdb=" CA HIS A 276 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N GLY A 683 " pdb=" CA GLY A 683 " pdb=" C GLY A 683 " ideal model delta sigma weight residual 113.18 104.39 8.79 2.37e+00 1.78e-01 1.38e+01 angle pdb=" N THR A 376 " pdb=" CA THR A 376 " pdb=" C THR A 376 " ideal model delta sigma weight residual 108.65 113.64 -4.99 1.85e+00 2.92e-01 7.27e+00 angle pdb=" C LEU A 543 " pdb=" N VAL A 544 " pdb=" CA VAL A 544 " ideal model delta sigma weight residual 120.56 117.30 3.26 1.26e+00 6.30e-01 6.71e+00 angle pdb=" CA LEU A 696 " pdb=" CB LEU A 696 " pdb=" CG LEU A 696 " ideal model delta sigma weight residual 116.30 125.10 -8.80 3.50e+00 8.16e-02 6.32e+00 ... (remaining 14239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5518 17.93 - 35.87: 438 35.87 - 53.80: 76 53.80 - 71.73: 8 71.73 - 89.66: 12 Dihedral angle restraints: 6052 sinusoidal: 2321 harmonic: 3731 Sorted by residual: dihedral pdb=" CA ASP A 682 " pdb=" C ASP A 682 " pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" N THR A 376 " pdb=" CA THR A 376 " ideal model delta harmonic sigma weight residual -180.00 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 775 0.035 - 0.070: 521 0.070 - 0.105: 170 0.105 - 0.140: 42 0.140 - 0.175: 7 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA GLN A 500 " pdb=" N GLN A 500 " pdb=" C GLN A 500 " pdb=" CB GLN A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CG LEU B 499 " pdb=" CB LEU B 499 " pdb=" CD1 LEU B 499 " pdb=" CD2 LEU B 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA GLN B 500 " pdb=" N GLN B 500 " pdb=" C GLN B 500 " pdb=" CB GLN B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1512 not shown) Planarity restraints: 1874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 370 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO A 371 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 149 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO A 150 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 509 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 510 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.028 5.00e-02 4.00e+02 ... (remaining 1871 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 595 2.71 - 3.26: 10370 3.26 - 3.81: 16231 3.81 - 4.35: 20717 4.35 - 4.90: 35683 Nonbonded interactions: 83596 Sorted by model distance: nonbonded pdb=" O TRP A 341 " pdb=" NE2 GLN A 352 " model vdw 2.167 3.120 nonbonded pdb=" NH2 ARG B 249 " pdb=" OD2 ASP B 387 " model vdw 2.191 3.120 nonbonded pdb=" O THR A 275 " pdb=" ND1 HIS A 276 " model vdw 2.195 3.120 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.248 3.040 nonbonded pdb=" O SER B 140 " pdb=" OG SER B 140 " model vdw 2.251 3.040 ... (remaining 83591 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 40 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 165 or (resid 166 and (name N or n \ ame CA or name C or name O or name CB )) or resid 167 through 178 or (resid 179 \ and (name N or name CA or name C or name O or name CB )) or resid 180 through 19 \ 6 or resid 240 through 326 or (resid 327 and (name N or name CA or name C or nam \ e O or name CB )) or resid 328 through 515 or (resid 516 and (name N or name CA \ or name C or name O or name CB )) or resid 517 through 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 589 or (r \ esid 590 through 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 801)) selection = (chain 'B' and (resid 40 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 193 or (resid 194 through 195 and \ (name N or name CA or name C or name O or name CB )) or resid 196 or resid 240 t \ hrough 252 or (resid 253 and (name N or name CA or name C or name O or name CB ) \ ) or resid 254 through 282 or (resid 283 and (name N or name CA or name C or nam \ e O or name CB )) or resid 284 through 286 or (resid 287 and (name N or name CA \ or name C or name O or name CB )) or resid 288 through 341 or (resid 342 through \ 343 and (name N or name CA or name C or name O or name CB )) or resid 344 throu \ gh 346 or resid 351 through 352 or (resid 353 and (name N or name CA or name C o \ r name O or name CB )) or resid 354 through 367 or (resid 368 and (name N or nam \ e CA or name C or name O or name CB )) or resid 369 through 801)) } 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: 3.740 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: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.200 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.012 0.604 10427 Z= 0.384 Angle : 0.755 8.799 14244 Z= 0.394 Chirality : 0.049 0.175 1515 Planarity : 0.005 0.053 1874 Dihedral : 13.719 89.664 3674 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -2.02 (0.22), residues: 1314 helix: -0.81 (0.21), residues: 544 sheet: -1.46 (1.24), residues: 20 loop : -1.79 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 705 TYR 0.018 0.002 TYR A 155 PHE 0.023 0.002 PHE B 332 TRP 0.029 0.002 TRP A 39 HIS 0.008 0.002 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00914 (10425) covalent geometry : angle 0.75456 (14244) hydrogen bonds : bond 0.18696 ( 373) hydrogen bonds : angle 6.49371 ( 1026) Misc. bond : bond 0.53979 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1116 time to fit residues: 12.9860 Evaluate side-chains 72 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096464 restraints weight = 15835.638| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.04 r_work: 0.3120 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.290 10427 Z= 0.126 Angle : 0.588 13.279 14244 Z= 0.285 Chirality : 0.041 0.130 1515 Planarity : 0.005 0.057 1874 Dihedral : 5.688 67.131 1436 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.69 % Allowed : 4.82 % Favored : 94.49 % 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: -1.45 (0.22), residues: 1314 helix: -0.22 (0.22), residues: 546 sheet: -0.47 (1.38), residues: 20 loop : -1.58 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.012 0.001 TYR A 155 PHE 0.011 0.001 PHE B 657 TRP 0.012 0.001 TRP A 149 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00292 (10425) covalent geometry : angle 0.58774 (14244) hydrogen bonds : bond 0.04400 ( 373) hydrogen bonds : angle 4.68461 ( 1026) Misc. bond : bond 0.25018 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.515 Fit side-chains REVERT: B 535 ASN cc_start: 0.8241 (t0) cc_final: 0.8030 (t0) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 0.1068 time to fit residues: 13.7664 Evaluate side-chains 81 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091414 restraints weight = 16163.871| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.09 r_work: 0.3029 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.211 10427 Z= 0.331 Angle : 0.709 15.878 14244 Z= 0.342 Chirality : 0.048 0.160 1515 Planarity : 0.005 0.054 1874 Dihedral : 6.041 71.236 1436 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.69 % Allowed : 8.66 % Favored : 90.65 % 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: -1.48 (0.22), residues: 1314 helix: -0.23 (0.22), residues: 541 sheet: -0.89 (1.30), residues: 20 loop : -1.60 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 705 TYR 0.021 0.002 TYR A 155 PHE 0.021 0.002 PHE B 332 TRP 0.016 0.002 TRP B 90 HIS 0.008 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00800 (10425) covalent geometry : angle 0.70881 (14244) hydrogen bonds : bond 0.05172 ( 373) hydrogen bonds : angle 4.73102 ( 1026) Misc. bond : bond 0.15973 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.391 Fit side-chains REVERT: B 254 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7981 (mtp-110) REVERT: B 535 ASN cc_start: 0.8354 (t0) cc_final: 0.8048 (t0) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.1055 time to fit residues: 11.8990 Evaluate side-chains 78 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 612 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.114699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095316 restraints weight = 15892.732| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.06 r_work: 0.3116 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 10427 Z= 0.119 Angle : 0.559 13.536 14244 Z= 0.268 Chirality : 0.040 0.130 1515 Planarity : 0.005 0.053 1874 Dihedral : 5.413 66.782 1436 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.89 % Allowed : 10.53 % Favored : 88.58 % 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: -1.17 (0.22), residues: 1314 helix: 0.13 (0.23), residues: 540 sheet: -0.77 (1.21), residues: 20 loop : -1.49 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 640 TYR 0.013 0.001 TYR A 155 PHE 0.011 0.001 PHE B 657 TRP 0.008 0.001 TRP B 90 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00285 (10425) covalent geometry : angle 0.55913 (14244) hydrogen bonds : bond 0.03762 ( 373) hydrogen bonds : angle 4.36508 ( 1026) Misc. bond : bond 0.16017 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.286 Fit side-chains REVERT: B 513 ASP cc_start: 0.7618 (p0) cc_final: 0.7241 (p0) REVERT: B 535 ASN cc_start: 0.8231 (t0) cc_final: 0.7957 (t0) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.0924 time to fit residues: 11.8819 Evaluate side-chains 87 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 420 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 0.0030 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.115301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095731 restraints weight = 15825.583| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.09 r_work: 0.3127 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 10427 Z= 0.110 Angle : 0.538 12.539 14244 Z= 0.255 Chirality : 0.040 0.132 1515 Planarity : 0.004 0.048 1874 Dihedral : 5.192 67.467 1436 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.18 % Allowed : 11.91 % Favored : 86.91 % 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: -0.97 (0.23), residues: 1314 helix: 0.34 (0.23), residues: 546 sheet: -0.48 (1.16), residues: 20 loop : -1.44 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.014 0.001 TYR A 155 PHE 0.007 0.001 PHE B 272 TRP 0.009 0.001 TRP B 341 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00263 (10425) covalent geometry : angle 0.53771 (14244) hydrogen bonds : bond 0.03456 ( 373) hydrogen bonds : angle 4.16015 ( 1026) Misc. bond : bond 0.16372 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.368 Fit side-chains REVERT: A 516 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8538 (tptp) REVERT: B 513 ASP cc_start: 0.7599 (p0) cc_final: 0.7286 (p0) REVERT: B 535 ASN cc_start: 0.8212 (t0) cc_final: 0.7905 (t0) REVERT: B 656 ASP cc_start: 0.8419 (m-30) cc_final: 0.8212 (m-30) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1004 time to fit residues: 13.5857 Evaluate side-chains 91 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 0.0070 chunk 130 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097092 restraints weight = 15921.246| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.07 r_work: 0.3129 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 10427 Z= 0.116 Angle : 0.536 12.235 14244 Z= 0.255 Chirality : 0.040 0.178 1515 Planarity : 0.004 0.044 1874 Dihedral : 5.134 67.597 1436 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.18 % Allowed : 12.80 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.23), residues: 1314 helix: 0.48 (0.23), residues: 545 sheet: -0.39 (1.14), residues: 20 loop : -1.40 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 254 TYR 0.014 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.008 0.001 TRP B 90 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00282 (10425) covalent geometry : angle 0.53630 (14244) hydrogen bonds : bond 0.03458 ( 373) hydrogen bonds : angle 4.10823 ( 1026) Misc. bond : bond 0.16075 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.412 Fit side-chains REVERT: A 516 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8540 (tptp) REVERT: B 513 ASP cc_start: 0.7541 (p0) cc_final: 0.7237 (p0) REVERT: B 535 ASN cc_start: 0.8197 (t0) cc_final: 0.7850 (t0) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1093 time to fit residues: 14.5721 Evaluate side-chains 89 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 703 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.117799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098596 restraints weight = 15689.686| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.03 r_work: 0.3159 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 10427 Z= 0.104 Angle : 0.525 11.768 14244 Z= 0.249 Chirality : 0.040 0.160 1515 Planarity : 0.004 0.043 1874 Dihedral : 4.996 66.679 1436 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.18 % Allowed : 13.98 % Favored : 84.84 % 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: -0.67 (0.23), residues: 1314 helix: 0.67 (0.23), residues: 541 sheet: -0.20 (1.13), residues: 20 loop : -1.33 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.006 0.001 TRP B 341 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00247 (10425) covalent geometry : angle 0.52523 (14244) hydrogen bonds : bond 0.03246 ( 373) hydrogen bonds : angle 4.03256 ( 1026) Misc. bond : bond 0.16010 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.379 Fit side-chains REVERT: A 276 HIS cc_start: 0.4140 (OUTLIER) cc_final: 0.3473 (m90) REVERT: B 513 ASP cc_start: 0.7473 (p0) cc_final: 0.7220 (p0) REVERT: B 535 ASN cc_start: 0.8152 (t0) cc_final: 0.7816 (t0) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1060 time to fit residues: 14.8395 Evaluate side-chains 91 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.117822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098541 restraints weight = 15728.497| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.05 r_work: 0.3160 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 10427 Z= 0.108 Angle : 0.536 11.679 14244 Z= 0.255 Chirality : 0.040 0.157 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.964 67.119 1436 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.98 % Allowed : 14.67 % Favored : 84.35 % 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: -0.62 (0.23), residues: 1314 helix: 0.67 (0.23), residues: 548 sheet: -0.22 (1.13), residues: 20 loop : -1.29 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.014 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.007 0.001 TRP B 90 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00259 (10425) covalent geometry : angle 0.53648 (14244) hydrogen bonds : bond 0.03249 ( 373) hydrogen bonds : angle 3.99369 ( 1026) Misc. bond : bond 0.15759 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.344 Fit side-chains REVERT: A 327 LYS cc_start: 0.8243 (tptm) cc_final: 0.7650 (tppt) REVERT: B 513 ASP cc_start: 0.7480 (p0) cc_final: 0.7228 (p0) REVERT: B 535 ASN cc_start: 0.8167 (t0) cc_final: 0.7829 (t0) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.1000 time to fit residues: 12.8118 Evaluate side-chains 90 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 86 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.116853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097331 restraints weight = 15667.513| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.09 r_work: 0.3160 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 10427 Z= 0.105 Angle : 0.535 11.506 14244 Z= 0.255 Chirality : 0.040 0.158 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.922 66.821 1436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.38 % Allowed : 14.57 % Favored : 84.06 % 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: -0.60 (0.23), residues: 1314 helix: 0.71 (0.23), residues: 550 sheet: -0.06 (1.14), residues: 20 loop : -1.30 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.006 0.001 TRP B 90 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00251 (10425) covalent geometry : angle 0.53526 (14244) hydrogen bonds : bond 0.03193 ( 373) hydrogen bonds : angle 3.96924 ( 1026) Misc. bond : bond 0.15629 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.282 Fit side-chains REVERT: A 327 LYS cc_start: 0.8269 (tptm) cc_final: 0.7650 (tppt) REVERT: B 513 ASP cc_start: 0.7514 (p0) cc_final: 0.7251 (p0) REVERT: B 535 ASN cc_start: 0.8168 (t0) cc_final: 0.7821 (t0) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.1061 time to fit residues: 14.3641 Evaluate side-chains 89 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099204 restraints weight = 15551.033| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.01 r_work: 0.3169 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 10427 Z= 0.109 Angle : 0.541 11.491 14244 Z= 0.258 Chirality : 0.040 0.160 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.914 66.908 1436 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.18 % Allowed : 14.67 % Favored : 84.15 % 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: -0.56 (0.23), residues: 1314 helix: 0.77 (0.23), residues: 546 sheet: -0.05 (1.14), residues: 20 loop : -1.29 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.012 0.001 TRP B 397 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00260 (10425) covalent geometry : angle 0.54057 (14244) hydrogen bonds : bond 0.03195 ( 373) hydrogen bonds : angle 3.95410 ( 1026) Misc. bond : bond 0.15399 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.339 Fit side-chains REVERT: A 327 LYS cc_start: 0.8243 (tptm) cc_final: 0.7605 (tppt) REVERT: A 333 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7330 (mt) REVERT: B 368 PHE cc_start: 0.7672 (m-10) cc_final: 0.7367 (m-10) REVERT: B 513 ASP cc_start: 0.7543 (p0) cc_final: 0.7269 (p0) REVERT: B 535 ASN cc_start: 0.8145 (t0) cc_final: 0.7786 (t0) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.1004 time to fit residues: 13.1007 Evaluate side-chains 89 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.116517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097027 restraints weight = 15634.496| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.06 r_work: 0.3154 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 10427 Z= 0.115 Angle : 0.543 11.546 14244 Z= 0.259 Chirality : 0.040 0.165 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.933 67.169 1436 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.08 % Allowed : 14.86 % Favored : 84.06 % 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: -0.55 (0.23), residues: 1314 helix: 0.78 (0.23), residues: 547 sheet: -0.06 (1.14), residues: 20 loop : -1.29 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 254 TYR 0.014 0.001 TYR A 155 PHE 0.007 0.001 PHE A 129 TRP 0.012 0.001 TRP B 397 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00279 (10425) covalent geometry : angle 0.54267 (14244) hydrogen bonds : bond 0.03277 ( 373) hydrogen bonds : angle 3.94558 ( 1026) Misc. bond : bond 0.15171 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.04 seconds wall clock time: 41 minutes 27.76 seconds (2487.76 seconds total)