Starting phenix.real_space_refine on Fri Feb 14 13:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a7a_11676/02_2025/7a7a_11676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a7a_11676/02_2025/7a7a_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_11676/02_2025/7a7a_11676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a7a_11676/02_2025/7a7a_11676.map" model { file = "/net/cci-nas-00/data/ceres_data/7a7a_11676/02_2025/7a7a_11676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a7a_11676/02_2025/7a7a_11676.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP: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: 6.30, per 1000 atoms: 0.62 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: 2.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.05 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: 2.68 Time building geometry restraints manager: 3.07 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 739 or resid 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 739 or resid 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: 3.250 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.830 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- 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 : 0.009 0.082 10425 Z= 0.602 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.002 TRP A 39 HIS 0.008 0.002 HIS A 276 PHE 0.023 0.002 PHE B 332 TYR 0.018 0.002 TYR A 155 ARG 0.008 0.001 ARG A 705 *********************** 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 : 1.604 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2649 time to fit residues: 31.4128 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 : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 0.0370 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.115449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096163 restraints weight = 15701.586| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.08 r_work: 0.3140 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10425 Z= 0.175 Angle : 0.575 12.382 14244 Z= 0.280 Chirality : 0.040 0.128 1515 Planarity : 0.005 0.056 1874 Dihedral : 5.574 66.196 1436 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.59 % Allowed : 4.63 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1314 helix: -0.16 (0.22), residues: 542 sheet: -0.43 (1.36), residues: 20 loop : -1.57 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.005 0.001 HIS A 276 PHE 0.013 0.001 PHE B 657 TYR 0.010 0.001 TYR A 155 ARG 0.003 0.000 ARG A 595 *********************** 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: 6 poor density : 84 time to evaluate : 1.273 Fit side-chains REVERT: B 513 ASP cc_start: 0.7664 (p0) cc_final: 0.7266 (p0) REVERT: B 535 ASN cc_start: 0.8238 (t0) cc_final: 0.8018 (t0) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.2406 time to fit residues: 30.8708 Evaluate side-chains 79 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 64 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092904 restraints weight = 16106.994| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.06 r_work: 0.3065 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10425 Z= 0.418 Angle : 0.656 15.130 14244 Z= 0.315 Chirality : 0.045 0.148 1515 Planarity : 0.005 0.053 1874 Dihedral : 5.819 70.335 1436 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.69 % Allowed : 8.46 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1314 helix: -0.21 (0.22), residues: 554 sheet: -0.89 (1.30), residues: 20 loop : -1.58 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 90 HIS 0.008 0.001 HIS A 276 PHE 0.017 0.002 PHE B 332 TYR 0.019 0.001 TYR A 155 ARG 0.006 0.000 ARG A 705 *********************** 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 82 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.096 Fit side-chains REVERT: B 535 ASN cc_start: 0.8312 (t0) cc_final: 0.8021 (t0) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.2224 time to fit residues: 25.6001 Evaluate side-chains 79 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.116634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097814 restraints weight = 15743.648| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.98 r_work: 0.3140 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10425 Z= 0.191 Angle : 0.549 13.108 14244 Z= 0.262 Chirality : 0.040 0.131 1515 Planarity : 0.004 0.050 1874 Dihedral : 5.323 66.991 1436 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.98 % Allowed : 9.55 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1314 helix: 0.16 (0.22), residues: 545 sheet: -0.64 (1.24), residues: 20 loop : -1.48 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.006 0.001 HIS A 276 PHE 0.011 0.001 PHE B 657 TYR 0.013 0.001 TYR A 155 ARG 0.004 0.000 ARG B 254 *********************** 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 96 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.088 Fit side-chains REVERT: B 368 PHE cc_start: 0.7552 (m-10) cc_final: 0.7267 (m-10) REVERT: B 513 ASP cc_start: 0.7601 (p0) cc_final: 0.7243 (p0) REVERT: B 535 ASN cc_start: 0.8202 (t0) cc_final: 0.7919 (t0) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.2197 time to fit residues: 28.9521 Evaluate side-chains 89 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.112844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093197 restraints weight = 15777.299| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.08 r_work: 0.3086 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10425 Z= 0.285 Angle : 0.577 13.522 14244 Z= 0.275 Chirality : 0.042 0.135 1515 Planarity : 0.005 0.048 1874 Dihedral : 5.432 69.010 1436 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.48 % Allowed : 11.12 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1314 helix: 0.16 (0.22), residues: 554 sheet: -0.78 (1.20), residues: 20 loop : -1.51 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 90 HIS 0.006 0.001 HIS A 276 PHE 0.011 0.001 PHE B 332 TYR 0.017 0.001 TYR A 155 ARG 0.004 0.000 ARG B 254 *********************** 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 94 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.067 Fit side-chains REVERT: B 513 ASP cc_start: 0.7644 (p0) cc_final: 0.7266 (p0) REVERT: B 535 ASN cc_start: 0.8243 (t0) cc_final: 0.7923 (t0) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.2132 time to fit residues: 28.3014 Evaluate side-chains 89 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 282 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 15 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097366 restraints weight = 15760.170| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.03 r_work: 0.3135 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10425 Z= 0.184 Angle : 0.537 12.488 14244 Z= 0.255 Chirality : 0.040 0.131 1515 Planarity : 0.004 0.046 1874 Dihedral : 5.170 66.984 1436 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.28 % Allowed : 12.50 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1314 helix: 0.45 (0.23), residues: 540 sheet: -0.64 (1.14), residues: 20 loop : -1.41 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.005 0.001 HIS A 276 PHE 0.007 0.001 PHE A 129 TYR 0.014 0.001 TYR A 155 ARG 0.004 0.000 ARG B 254 *********************** 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 95 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.073 Fit side-chains REVERT: B 513 ASP cc_start: 0.7487 (p0) cc_final: 0.7198 (p0) REVERT: B 535 ASN cc_start: 0.8166 (t0) cc_final: 0.7852 (t0) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.2325 time to fit residues: 30.5701 Evaluate side-chains 93 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 0.0670 chunk 125 optimal weight: 5.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.117415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097743 restraints weight = 15667.247| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.11 r_work: 0.3162 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10425 Z= 0.151 Angle : 0.522 11.681 14244 Z= 0.248 Chirality : 0.039 0.130 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.955 66.630 1436 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.18 % Allowed : 13.39 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1314 helix: 0.69 (0.23), residues: 541 sheet: -0.34 (1.13), residues: 20 loop : -1.36 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 341 HIS 0.002 0.000 HIS A 49 PHE 0.007 0.001 PHE A 129 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG B 254 *********************** 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 : 1.171 Fit side-chains REVERT: A 254 ARG cc_start: 0.8749 (ptp-170) cc_final: 0.8546 (ptp90) REVERT: A 327 LYS cc_start: 0.8204 (tptm) cc_final: 0.7587 (tppt) REVERT: B 513 ASP cc_start: 0.7599 (p0) cc_final: 0.7290 (p0) REVERT: B 535 ASN cc_start: 0.8171 (t0) cc_final: 0.7830 (t0) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.2249 time to fit residues: 31.1884 Evaluate side-chains 90 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 420 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 732 MET 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 45 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.116909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097357 restraints weight = 15826.986| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.07 r_work: 0.3144 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10425 Z= 0.214 Angle : 0.551 12.134 14244 Z= 0.262 Chirality : 0.041 0.130 1515 Planarity : 0.004 0.044 1874 Dihedral : 5.057 67.900 1436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.08 % Allowed : 14.47 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1314 helix: 0.59 (0.23), residues: 548 sheet: -0.34 (1.13), residues: 20 loop : -1.34 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 90 HIS 0.003 0.001 HIS B 49 PHE 0.008 0.001 PHE B 332 TYR 0.015 0.001 TYR A 155 ARG 0.005 0.000 ARG B 254 *********************** 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: 11 poor density : 81 time to evaluate : 1.085 Fit side-chains REVERT: A 327 LYS cc_start: 0.8239 (tptm) cc_final: 0.7641 (tppt) REVERT: B 513 ASP cc_start: 0.7531 (p0) cc_final: 0.7224 (p0) REVERT: B 535 ASN cc_start: 0.8153 (t0) cc_final: 0.7802 (t0) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.2300 time to fit residues: 28.9845 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 : 1.180 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.115809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096023 restraints weight = 15751.842| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.12 r_work: 0.3159 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10425 Z= 0.201 Angle : 0.552 11.644 14244 Z= 0.264 Chirality : 0.041 0.152 1515 Planarity : 0.004 0.044 1874 Dihedral : 5.035 67.271 1436 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.08 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1314 helix: 0.65 (0.23), residues: 550 sheet: -0.35 (1.12), residues: 20 loop : -1.35 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 90 HIS 0.003 0.000 HIS B 49 PHE 0.007 0.001 PHE A 129 TYR 0.014 0.001 TYR A 155 ARG 0.006 0.000 ARG B 254 *********************** 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 90 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.100 Fit side-chains REVERT: A 327 LYS cc_start: 0.8281 (tptm) cc_final: 0.7683 (tppt) REVERT: B 513 ASP cc_start: 0.7504 (p0) cc_final: 0.7206 (p0) REVERT: B 535 ASN cc_start: 0.8175 (t0) cc_final: 0.7831 (t0) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.2245 time to fit residues: 28.1928 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 : 1.232 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.115449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095761 restraints weight = 15712.125| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.09 r_work: 0.3132 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10425 Z= 0.209 Angle : 0.554 11.801 14244 Z= 0.264 Chirality : 0.041 0.170 1515 Planarity : 0.004 0.044 1874 Dihedral : 5.057 67.540 1436 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.98 % Allowed : 14.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1314 helix: 0.70 (0.23), residues: 544 sheet: -0.35 (1.13), residues: 20 loop : -1.34 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 90 HIS 0.003 0.000 HIS B 49 PHE 0.008 0.001 PHE B 332 TYR 0.015 0.001 TYR A 155 ARG 0.007 0.000 ARG B 254 ********************** 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 87 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.054 Fit side-chains REVERT: A 327 LYS cc_start: 0.8252 (tptm) cc_final: 0.7645 (tppt) REVERT: B 513 ASP cc_start: 0.7523 (p0) cc_final: 0.7212 (p0) REVERT: B 535 ASN cc_start: 0.8176 (t0) cc_final: 0.7823 (t0) outliers start: 10 outliers final: 10 residues processed: 83 average time/residue: 0.2404 time to fit residues: 29.1746 Evaluate side-chains 87 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.117924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098710 restraints weight = 15639.145| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.01 r_work: 0.3153 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10425 Z= 0.188 Angle : 0.545 11.764 14244 Z= 0.259 Chirality : 0.040 0.166 1515 Planarity : 0.004 0.043 1874 Dihedral : 4.985 67.081 1436 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.18 % Allowed : 14.57 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1314 helix: 0.74 (0.23), residues: 544 sheet: -0.21 (1.13), residues: 20 loop : -1.33 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.002 0.000 HIS B 49 PHE 0.007 0.001 PHE A 129 TYR 0.014 0.001 TYR A 155 ARG 0.006 0.000 ARG B 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4517.69 seconds wall clock time: 80 minutes 58.03 seconds (4858.03 seconds total)