Starting phenix.real_space_refine (version: dev) on Tue Apr 5 01:23:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_11676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_11676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_11676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_11676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/04_2022/7a7a_11676_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 6.19, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.19 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 66 helices and 2 sheets defined 41.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.557A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.487A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.830A pdb=" N MET A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 383 through 386 No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'A' and resid 388 through 398 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 401 through 417 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 454 through 463 Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 503 No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 514 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 540 through 559 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 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 633 removed outlier: 4.033A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.974A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 734 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 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 149 through 158 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) removed outlier: 7.055A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LYS B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 175 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 241 through 253 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 259 through 269 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 388 through 398 removed outlier: 4.704A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 452 through 463 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 469 through 480 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 515 through 530 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 540 through 556 removed outlier: 3.798A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 633 removed outlier: 3.747A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 693 through 700 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 702 through 711 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 718 through 732 Processing sheet with id= A, first strand: chain 'B' and resid 341 through 345 Processing sheet with id= B, first strand: chain 'B' and resid 667 through 670 280 hydrogen bonds defined for protein. 831 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: 2.73 Time building geometry restraints manager: 4.56 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: 89.00 - 107.02: 430 107.02 - 125.05: 13468 125.05 - 143.08: 342 143.08 - 161.11: 0 161.11 - 179.14: 4 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: 600 2.71 - 3.26: 10435 3.26 - 3.81: 16317 3.81 - 4.35: 20913 4.35 - 4.90: 35703 Nonbonded interactions: 83968 Sorted by model distance: nonbonded pdb=" O TRP A 341 " pdb=" NE2 GLN A 352 " model vdw 2.167 2.520 nonbonded pdb=" NH2 ARG B 249 " pdb=" OD2 ASP B 387 " model vdw 2.191 2.520 nonbonded pdb=" O THR A 275 " pdb=" ND1 HIS A 276 " model vdw 2.195 2.520 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.248 2.440 nonbonded pdb=" O SER B 140 " pdb=" OG SER B 140 " model vdw 2.251 2.440 ... (remaining 83963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 4.630 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: 0.020 Extract box with map and model: 12.350 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 30.380 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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= 0.590 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 : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.00 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2404 time to fit residues: 28.7548 Evaluate side-chains 71 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8138 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.0000 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 10425 Z= 0.186 Angle : 0.561 12.343 14244 Z= 0.269 Chirality : 0.040 0.130 1515 Planarity : 0.005 0.111 1874 Dihedral : 5.590 67.426 1436 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.69 % 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: -1.52 (0.22), residues: 1314 helix: -0.25 (0.22), residues: 551 sheet: -0.48 (1.32), residues: 20 loop : -1.66 (0.21), residues: 743 *********************** 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 97 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.305 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.2099 time to fit residues: 29.0343 Evaluate side-chains 84 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0974 time to fit residues: 2.2163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 overall best weight: 0.7552 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 10425 Z= 0.185 Angle : 0.538 12.245 14244 Z= 0.255 Chirality : 0.040 0.129 1515 Planarity : 0.005 0.119 1874 Dihedral : 5.331 68.062 1436 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1314 helix: 0.07 (0.23), residues: 548 sheet: -0.47 (1.32), residues: 20 loop : -1.56 (0.21), residues: 746 *********************** 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 84 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.230 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 83 average time/residue: 0.2249 time to fit residues: 27.7383 Evaluate side-chains 78 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0984 time to fit residues: 1.8115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 10425 Z= 0.296 Angle : 0.577 13.453 14244 Z= 0.273 Chirality : 0.042 0.137 1515 Planarity : 0.005 0.090 1874 Dihedral : 5.447 69.390 1436 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.59 % 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: -1.23 (0.23), residues: 1314 helix: 0.06 (0.23), residues: 553 sheet: -0.78 (1.19), residues: 20 loop : -1.55 (0.22), residues: 741 *********************** 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 82 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.248 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.2204 time to fit residues: 26.1681 Evaluate side-chains 78 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0966 time to fit residues: 2.2440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 10425 Z= 0.182 Angle : 0.527 12.139 14244 Z= 0.249 Chirality : 0.040 0.162 1515 Planarity : 0.005 0.076 1874 Dihedral : 5.116 67.430 1436 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.23), residues: 1314 helix: 0.30 (0.23), residues: 548 sheet: -0.65 (1.15), residues: 20 loop : -1.52 (0.22), residues: 746 *********************** 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 86 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.155 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 84 average time/residue: 0.2195 time to fit residues: 27.1084 Evaluate side-chains 82 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1006 time to fit residues: 2.3034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.0770 chunk 114 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.0000 chunk 10 optimal weight: 0.0870 chunk 41 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 10425 Z= 0.166 Angle : 0.504 10.973 14244 Z= 0.239 Chirality : 0.038 0.133 1515 Planarity : 0.004 0.066 1874 Dihedral : 4.807 66.101 1436 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.79 % 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: -0.77 (0.23), residues: 1314 helix: 0.65 (0.23), residues: 547 sheet: -0.22 (1.16), residues: 20 loop : -1.46 (0.21), residues: 747 *********************** 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 105 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.056 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.1953 time to fit residues: 29.3393 Evaluate side-chains 89 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0963 time to fit residues: 1.9202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 10425 Z= 0.335 Angle : 0.602 12.829 14244 Z= 0.292 Chirality : 0.042 0.142 1515 Planarity : 0.005 0.088 1874 Dihedral : 5.140 69.009 1436 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.30 % 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: -0.88 (0.23), residues: 1314 helix: 0.45 (0.23), residues: 555 sheet: -0.61 (1.11), residues: 20 loop : -1.44 (0.22), residues: 739 *********************** 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 85 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.237 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.2227 time to fit residues: 27.9270 Evaluate side-chains 81 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1034 time to fit residues: 1.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.156 10425 Z= 0.216 Angle : 0.552 11.491 14244 Z= 0.266 Chirality : 0.040 0.144 1515 Planarity : 0.005 0.087 1874 Dihedral : 4.938 66.969 1436 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.30 % 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: -0.77 (0.23), residues: 1314 helix: 0.62 (0.23), residues: 550 sheet: -0.43 (1.13), residues: 20 loop : -1.45 (0.22), residues: 744 *********************** 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 84 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.156 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.2306 time to fit residues: 28.8872 Evaluate side-chains 80 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1000 time to fit residues: 2.0163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.174 10425 Z= 0.229 Angle : 0.560 12.092 14244 Z= 0.273 Chirality : 0.040 0.149 1515 Planarity : 0.005 0.101 1874 Dihedral : 4.930 67.725 1436 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.30 % 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: -0.76 (0.23), residues: 1314 helix: 0.64 (0.23), residues: 552 sheet: -0.35 (1.13), residues: 20 loop : -1.45 (0.22), residues: 742 *********************** 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 84 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.167 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 0.2439 time to fit residues: 29.4633 Evaluate side-chains 83 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1064 time to fit residues: 2.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 63 optimal weight: 0.0570 chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 10425 Z= 0.187 Angle : 0.535 10.725 14244 Z= 0.258 Chirality : 0.039 0.156 1515 Planarity : 0.005 0.092 1874 Dihedral : 4.702 66.030 1436 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.00 % 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: -0.55 (0.23), residues: 1314 helix: 0.95 (0.24), residues: 540 sheet: -0.15 (1.16), residues: 20 loop : -1.42 (0.21), residues: 754 ********************** 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 89 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2354 time to fit residues: 30.5109 Evaluate side-chains 80 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.116206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096414 restraints weight = 15507.715| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.08 r_work: 0.3234 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3210 rms_B_bonded: 1.92 restraints_weight: 0.1250 r_work: 0.3197 rms_B_bonded: 2.01 restraints_weight: 0.0625 r_work: 0.3183 rms_B_bonded: 2.14 restraints_weight: 0.0312 r_work: 0.3167 rms_B_bonded: 2.30 restraints_weight: 0.0156 r_work: 0.3151 rms_B_bonded: 2.51 restraints_weight: 0.0078 r_work: 0.3133 rms_B_bonded: 2.75 restraints_weight: 0.0039 r_work: 0.3113 rms_B_bonded: 3.04 restraints_weight: 0.0020 r_work: 0.3092 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.3068 rms_B_bonded: 3.77 restraints_weight: 0.0005 r_work: 0.3042 rms_B_bonded: 4.23 restraints_weight: 0.0002 r_work: 0.3013 rms_B_bonded: 4.75 restraints_weight: 0.0001 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.164 10425 Z= 0.232 Angle : 0.570 13.492 14244 Z= 0.278 Chirality : 0.041 0.207 1515 Planarity : 0.005 0.120 1874 Dihedral : 4.857 68.143 1436 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.23), residues: 1314 helix: 0.87 (0.23), residues: 544 sheet: -0.21 (1.13), residues: 20 loop : -1.38 (0.22), residues: 750 =============================================================================== Job complete usr+sys time: 1930.85 seconds wall clock time: 35 minutes 56.03 seconds (2156.03 seconds total)