Starting phenix.real_space_refine on Wed Sep 25 19:08:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/09_2024/6of4_20042.cif" } resolution = 3.2 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= 0.018 sd= 0.673 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7028 2.51 5 N 1920 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10998 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Restraints were copied for chains: E, D Time building chain proxies: 8.60, per 1000 atoms: 0.78 Number of scatterers: 10998 At special positions: 0 Unit cell: (146.88, 89.64, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1996 8.00 N 1920 7.00 C 7028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.501A pdb=" N ASN B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS B 333 " --> pdb=" O PRO B 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.633A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.239A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 211 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.502A pdb=" N ASN E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER E 296 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS E 334 " --> pdb=" O PRO E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 334' Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.632A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.238A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU E 658 " --> pdb=" O PRO E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 691 " --> pdb=" O LYS E 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU B 646 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 637 " --> pdb=" O HIS B 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 650 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 635 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG B 123 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 130 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 7.026A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 420 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU E 646 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 637 " --> pdb=" O HIS E 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 650 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE E 635 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG E 123 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 130 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358 removed outlier: 7.027A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 420 " --> pdb=" O ILE E 263 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1392 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: 3.21 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3528 1.34 - 1.45: 1629 1.45 - 1.57: 6051 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 11296 Sorted by residual: bond pdb=" C ALA E 535 " pdb=" N PRO E 536 " ideal model delta sigma weight residual 1.335 1.309 0.026 1.38e-02 5.25e+03 3.49e+00 bond pdb=" C ALA B 535 " pdb=" N PRO B 536 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.38e-02 5.25e+03 3.38e+00 bond pdb=" CB TRP A 355 " pdb=" CG TRP A 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.04e+00 bond pdb=" CB TRP D 355 " pdb=" CG TRP D 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.01e+00 bond pdb=" CB TRP D 60 " pdb=" CG TRP D 60 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.74e+00 ... (remaining 11291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 14965 3.12 - 6.25: 418 6.25 - 9.37: 25 9.37 - 12.50: 0 12.50 - 15.62: 4 Bond angle restraints: 15412 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.67e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.48 -7.48 1.10e+00 8.26e-01 4.62e+01 angle pdb=" N ALA B 290 " pdb=" CA ALA B 290 " pdb=" C ALA B 290 " ideal model delta sigma weight residual 110.80 124.04 -13.24 2.13e+00 2.20e-01 3.86e+01 angle pdb=" N ALA E 290 " pdb=" CA ALA E 290 " pdb=" C ALA E 290 " ideal model delta sigma weight residual 110.80 124.02 -13.22 2.13e+00 2.20e-01 3.85e+01 angle pdb=" C HIS A 146 " pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 122.15 106.53 15.62 2.83e+00 1.25e-01 3.05e+01 ... (remaining 15407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6128 17.44 - 34.87: 436 34.87 - 52.31: 86 52.31 - 69.75: 78 69.75 - 87.18: 14 Dihedral angle restraints: 6742 sinusoidal: 2650 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ALA D 91 " pdb=" C ALA D 91 " pdb=" N GLY D 92 " pdb=" CA GLY D 92 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 6739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1012 0.048 - 0.096: 511 0.096 - 0.143: 149 0.143 - 0.191: 48 0.191 - 0.239: 6 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ALA B 290 " pdb=" N ALA B 290 " pdb=" C ALA B 290 " pdb=" CB ALA B 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ALA E 290 " pdb=" N ALA E 290 " pdb=" C ALA E 290 " pdb=" CB ALA E 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1723 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 330 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 331 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 331 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 331 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 330 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 331 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 509 " 0.042 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO E 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 510 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 187 2.65 - 3.21: 10602 3.21 - 3.78: 15009 3.78 - 4.34: 19213 4.34 - 4.90: 33309 Nonbonded interactions: 78320 Sorted by model distance: nonbonded pdb=" OG SER E 272 " pdb=" O MET E 424 " model vdw 2.091 3.040 nonbonded pdb=" OG SER B 272 " pdb=" O MET B 424 " model vdw 2.091 3.040 nonbonded pdb=" O SER B 444 " pdb=" OG1 THR B 445 " model vdw 2.170 3.040 nonbonded pdb=" O SER E 444 " pdb=" OG1 THR E 445 " model vdw 2.170 3.040 nonbonded pdb=" NH2 ARG E 201 " pdb=" OD1 ASN E 215 " model vdw 2.229 3.120 ... (remaining 78315 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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=0.20 max=1.00 mean=0.96 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: 0.530 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 28.710 Find NCS groups from input model: 0.260 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.010 0.064 11296 Z= 0.692 Angle : 1.187 15.624 15412 Z= 0.643 Chirality : 0.062 0.239 1726 Planarity : 0.009 0.073 1978 Dihedral : 15.119 87.184 4090 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 3.55 % Allowed : 19.61 % Favored : 76.85 % Rotamer: Outliers : 2.54 % Allowed : 6.44 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.99 (0.17), residues: 1382 helix: -2.88 (0.15), residues: 456 sheet: -1.37 (0.33), residues: 202 loop : -4.37 (0.18), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 297 HIS 0.008 0.002 HIS D 68 PHE 0.026 0.003 PHE A 107 TYR 0.034 0.004 TYR E 530 ARG 0.005 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 301 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 ASN cc_start: 0.7377 (t0) cc_final: 0.7076 (t0) REVERT: B 128 ARG cc_start: 0.6520 (ptt180) cc_final: 0.6009 (ptp-170) REVERT: B 139 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: B 156 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 164 ILE cc_start: 0.8876 (mt) cc_final: 0.8546 (pt) REVERT: B 183 THR cc_start: 0.7986 (m) cc_final: 0.7723 (t) REVERT: B 275 SER cc_start: 0.8651 (m) cc_final: 0.8430 (t) REVERT: B 557 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8849 (tp30) REVERT: B 723 VAL cc_start: 0.9126 (t) cc_final: 0.8848 (p) REVERT: E 109 MET cc_start: 0.3795 (mtm) cc_final: 0.3156 (tmm) REVERT: E 156 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8813 (tt) REVERT: E 183 THR cc_start: 0.8287 (m) cc_final: 0.7934 (t) REVERT: E 239 LEU cc_start: 0.7453 (tp) cc_final: 0.7247 (tt) REVERT: E 298 LYS cc_start: 0.8540 (mptt) cc_final: 0.8219 (mmtt) REVERT: E 349 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6570 (mp0) REVERT: E 376 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (tpp80) REVERT: E 557 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8901 (tp30) REVERT: E 665 GLU cc_start: 0.7645 (pt0) cc_final: 0.7202 (pt0) outliers start: 30 outliers final: 5 residues processed: 324 average time/residue: 0.2557 time to fit residues: 112.3069 Evaluate side-chains 197 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 376 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.0050 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 115 GLN B 144 ASN B 151 GLN B 174 HIS B 327 ASN D 62 GLN D 146 HIS E 115 GLN E 327 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11296 Z= 0.207 Angle : 0.825 11.703 15412 Z= 0.411 Chirality : 0.045 0.278 1726 Planarity : 0.007 0.058 1978 Dihedral : 6.680 86.075 1548 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.42 % Favored : 89.15 % Rotamer: Outliers : 3.47 % Allowed : 13.22 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.16 (0.23), residues: 1382 helix: 1.97 (0.22), residues: 478 sheet: -0.38 (0.33), residues: 256 loop : -3.29 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.013 0.001 HIS B 174 PHE 0.015 0.002 PHE B 312 TYR 0.017 0.002 TYR E 423 ARG 0.006 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 HIS cc_start: 0.7802 (t70) cc_final: 0.6830 (t70) REVERT: B 198 GLN cc_start: 0.8884 (tp40) cc_final: 0.8659 (tp40) REVERT: B 309 GLN cc_start: 0.8720 (pm20) cc_final: 0.8427 (pm20) REVERT: B 557 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8721 (tp30) REVERT: E 109 MET cc_start: 0.4673 (mtm) cc_final: 0.3527 (tmm) REVERT: E 128 ARG cc_start: 0.6358 (ptt180) cc_final: 0.5956 (ptp-170) REVERT: E 129 LEU cc_start: 0.7589 (mp) cc_final: 0.7316 (tt) REVERT: E 156 ILE cc_start: 0.8971 (mt) cc_final: 0.8759 (tt) REVERT: E 239 LEU cc_start: 0.7526 (tp) cc_final: 0.7294 (tt) REVERT: E 288 ASP cc_start: 0.8087 (t0) cc_final: 0.7817 (p0) REVERT: E 557 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8758 (tp30) outliers start: 41 outliers final: 23 residues processed: 259 average time/residue: 0.1987 time to fit residues: 76.8037 Evaluate side-chains 211 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 ASN Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 666 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN B 207 ASN B 242 HIS B 454 GLN E 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11296 Z= 0.226 Angle : 0.730 10.192 15412 Z= 0.360 Chirality : 0.044 0.176 1726 Planarity : 0.006 0.054 1978 Dihedral : 5.866 81.532 1528 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.35 % Favored : 89.22 % Rotamer: Outliers : 3.47 % Allowed : 15.93 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.09 (0.24), residues: 1382 helix: 3.01 (0.23), residues: 478 sheet: 0.01 (0.34), residues: 256 loop : -2.69 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 297 HIS 0.008 0.001 HIS B 532 PHE 0.017 0.002 PHE E 332 TYR 0.011 0.001 TYR E 482 ARG 0.006 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.214 Fit side-chains REVERT: B 174 HIS cc_start: 0.7586 (t70) cc_final: 0.6865 (t70) REVERT: B 306 ASP cc_start: 0.8737 (t70) cc_final: 0.8476 (t0) REVERT: B 309 GLN cc_start: 0.8685 (pm20) cc_final: 0.8301 (pm20) REVERT: B 557 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8802 (tp30) REVERT: E 109 MET cc_start: 0.4536 (mtm) cc_final: 0.3521 (tmm) REVERT: E 239 LEU cc_start: 0.7579 (tp) cc_final: 0.7318 (tt) REVERT: E 272 SER cc_start: 0.8435 (t) cc_final: 0.8144 (m) REVERT: E 557 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8779 (tp30) outliers start: 41 outliers final: 26 residues processed: 227 average time/residue: 0.1868 time to fit residues: 63.9341 Evaluate side-chains 213 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.0040 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 0.0570 chunk 112 optimal weight: 3.9990 overall best weight: 0.3328 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11296 Z= 0.150 Angle : 0.669 9.592 15412 Z= 0.329 Chirality : 0.042 0.205 1726 Planarity : 0.006 0.047 1978 Dihedral : 5.642 76.742 1528 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.32 % Favored : 91.39 % Rotamer: Outliers : 2.88 % Allowed : 17.20 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.21 (0.24), residues: 1382 helix: 3.10 (0.23), residues: 486 sheet: 0.09 (0.33), residues: 258 loop : -2.40 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 60 HIS 0.002 0.000 HIS B 357 PHE 0.024 0.001 PHE B 332 TYR 0.013 0.001 TYR E 423 ARG 0.006 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 1.644 Fit side-chains REVERT: A 66 CYS cc_start: 0.8449 (t) cc_final: 0.8247 (t) REVERT: B 174 HIS cc_start: 0.7347 (t70) cc_final: 0.6794 (t70) REVERT: B 185 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7207 (t0) REVERT: B 306 ASP cc_start: 0.8766 (t70) cc_final: 0.8473 (t0) REVERT: B 309 GLN cc_start: 0.8658 (pm20) cc_final: 0.8267 (pm20) REVERT: B 319 SER cc_start: 0.8010 (p) cc_final: 0.7720 (p) REVERT: B 512 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7506 (ttt90) REVERT: B 557 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8734 (tp30) REVERT: E 109 MET cc_start: 0.4322 (mtm) cc_final: 0.3309 (tmm) REVERT: E 136 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8270 (p) REVERT: E 239 LEU cc_start: 0.7608 (tp) cc_final: 0.7325 (tt) REVERT: E 272 SER cc_start: 0.8310 (t) cc_final: 0.8032 (m) REVERT: E 309 GLN cc_start: 0.8653 (pm20) cc_final: 0.8416 (pm20) REVERT: E 557 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8789 (tp30) outliers start: 34 outliers final: 15 residues processed: 222 average time/residue: 0.1861 time to fit residues: 63.1041 Evaluate side-chains 213 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 674 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11296 Z= 0.362 Angle : 0.728 9.812 15412 Z= 0.365 Chirality : 0.045 0.170 1726 Planarity : 0.006 0.053 1978 Dihedral : 5.603 75.153 1528 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.35 % Favored : 89.44 % Rotamer: Outliers : 3.47 % Allowed : 16.95 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.01 (0.24), residues: 1382 helix: 2.86 (0.23), residues: 488 sheet: -0.22 (0.31), residues: 262 loop : -2.40 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 171 HIS 0.009 0.001 HIS E 532 PHE 0.020 0.002 PHE E 332 TYR 0.015 0.002 TYR E 626 ARG 0.004 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.269 Fit side-chains REVERT: B 174 HIS cc_start: 0.7603 (t70) cc_final: 0.7176 (t70) REVERT: B 185 ASN cc_start: 0.8073 (m110) cc_final: 0.7641 (t0) REVERT: B 198 GLN cc_start: 0.9001 (tp40) cc_final: 0.8769 (tp-100) REVERT: B 306 ASP cc_start: 0.8738 (t70) cc_final: 0.8371 (t70) REVERT: B 309 GLN cc_start: 0.8634 (pm20) cc_final: 0.8266 (pm20) REVERT: B 512 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7445 (ttt90) REVERT: B 557 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8775 (tp30) REVERT: E 109 MET cc_start: 0.4157 (mtm) cc_final: 0.3436 (tmm) REVERT: E 239 LEU cc_start: 0.7687 (tp) cc_final: 0.7394 (tt) REVERT: E 309 GLN cc_start: 0.8633 (pm20) cc_final: 0.8372 (pm20) REVERT: E 512 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7525 (ttt90) REVERT: E 557 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8798 (tp30) outliers start: 41 outliers final: 29 residues processed: 225 average time/residue: 0.1845 time to fit residues: 62.6343 Evaluate side-chains 228 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11296 Z= 0.196 Angle : 0.654 8.858 15412 Z= 0.323 Chirality : 0.042 0.160 1726 Planarity : 0.006 0.049 1978 Dihedral : 5.101 43.926 1528 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 3.47 % Allowed : 18.22 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.15 (0.24), residues: 1382 helix: 3.00 (0.23), residues: 488 sheet: -0.11 (0.31), residues: 262 loop : -2.34 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 511 HIS 0.006 0.001 HIS E 532 PHE 0.016 0.002 PHE E 332 TYR 0.011 0.001 TYR E 423 ARG 0.006 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 1.191 Fit side-chains REVERT: A 362 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 174 HIS cc_start: 0.7427 (t70) cc_final: 0.7075 (t70) REVERT: B 185 ASN cc_start: 0.7782 (m110) cc_final: 0.7295 (t0) REVERT: B 306 ASP cc_start: 0.8720 (t70) cc_final: 0.8518 (t0) REVERT: B 512 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7431 (ttt90) REVERT: B 557 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8719 (tp30) REVERT: B 562 LEU cc_start: 0.9042 (mt) cc_final: 0.8836 (mt) REVERT: B 649 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7703 (pp) REVERT: D 362 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8755 (tt) REVERT: E 109 MET cc_start: 0.4478 (mtm) cc_final: 0.3429 (tmm) REVERT: E 239 LEU cc_start: 0.7702 (tp) cc_final: 0.7427 (tt) REVERT: E 306 ASP cc_start: 0.8702 (t0) cc_final: 0.8501 (t0) REVERT: E 309 GLN cc_start: 0.8594 (pm20) cc_final: 0.8256 (pm20) REVERT: E 557 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8860 (tp30) REVERT: E 649 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7695 (pp) outliers start: 41 outliers final: 21 residues processed: 223 average time/residue: 0.1756 time to fit residues: 60.4763 Evaluate side-chains 221 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11296 Z= 0.172 Angle : 0.643 8.700 15412 Z= 0.315 Chirality : 0.042 0.157 1726 Planarity : 0.006 0.046 1978 Dihedral : 4.881 33.455 1528 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 3.22 % Allowed : 18.39 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.25 (0.24), residues: 1382 helix: 3.07 (0.24), residues: 486 sheet: -0.01 (0.31), residues: 262 loop : -2.28 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 400 HIS 0.005 0.001 HIS E 532 PHE 0.014 0.001 PHE E 332 TYR 0.011 0.001 TYR B 423 ARG 0.005 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 1.241 Fit side-chains REVERT: A 362 ILE cc_start: 0.9099 (mt) cc_final: 0.8744 (tt) REVERT: B 174 HIS cc_start: 0.7303 (t70) cc_final: 0.6993 (t70) REVERT: B 185 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7233 (t0) REVERT: B 288 ASP cc_start: 0.8397 (t0) cc_final: 0.8085 (p0) REVERT: B 309 GLN cc_start: 0.8579 (pm20) cc_final: 0.8336 (pm20) REVERT: B 512 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7468 (ttt90) REVERT: B 557 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8719 (tp30) REVERT: B 649 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7654 (pp) REVERT: D 62 GLN cc_start: 0.8611 (tp40) cc_final: 0.8156 (tp-100) REVERT: D 362 ILE cc_start: 0.9092 (mt) cc_final: 0.8757 (tt) REVERT: E 109 MET cc_start: 0.4388 (mtm) cc_final: 0.3296 (tmm) REVERT: E 239 LEU cc_start: 0.7703 (tp) cc_final: 0.7411 (tt) REVERT: E 306 ASP cc_start: 0.8703 (t0) cc_final: 0.8470 (t0) REVERT: E 309 GLN cc_start: 0.8546 (pm20) cc_final: 0.8202 (pm20) REVERT: E 512 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7572 (ttt90) REVERT: E 557 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8851 (tp30) REVERT: E 649 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7655 (pp) outliers start: 38 outliers final: 24 residues processed: 229 average time/residue: 0.1848 time to fit residues: 64.4036 Evaluate side-chains 229 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11296 Z= 0.213 Angle : 0.660 8.700 15412 Z= 0.321 Chirality : 0.042 0.168 1726 Planarity : 0.005 0.043 1978 Dihedral : 4.836 32.388 1528 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.04 % Favored : 90.81 % Rotamer: Outliers : 3.05 % Allowed : 18.73 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.26 (0.24), residues: 1382 helix: 3.06 (0.24), residues: 486 sheet: 0.02 (0.31), residues: 262 loop : -2.25 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 400 HIS 0.004 0.001 HIS E 532 PHE 0.014 0.001 PHE E 265 TYR 0.009 0.001 TYR B 423 ARG 0.004 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.315 Fit side-chains REVERT: A 362 ILE cc_start: 0.9098 (mt) cc_final: 0.8761 (tt) REVERT: B 174 HIS cc_start: 0.7277 (t70) cc_final: 0.6984 (t70) REVERT: B 185 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7267 (t0) REVERT: B 309 GLN cc_start: 0.8600 (pm20) cc_final: 0.8312 (pm20) REVERT: B 512 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7548 (ttt90) REVERT: B 557 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8712 (tp30) REVERT: B 649 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7660 (pp) REVERT: D 362 ILE cc_start: 0.9098 (mt) cc_final: 0.8783 (tt) REVERT: E 109 MET cc_start: 0.4365 (mtm) cc_final: 0.3293 (tmm) REVERT: E 131 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7725 (pp) REVERT: E 239 LEU cc_start: 0.7760 (tp) cc_final: 0.7472 (tt) REVERT: E 306 ASP cc_start: 0.8648 (t0) cc_final: 0.8426 (t0) REVERT: E 309 GLN cc_start: 0.8543 (pm20) cc_final: 0.8321 (pm20) REVERT: E 512 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: E 557 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8871 (tp30) REVERT: E 649 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7744 (pp) outliers start: 36 outliers final: 28 residues processed: 223 average time/residue: 0.1775 time to fit residues: 60.9475 Evaluate side-chains 229 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11296 Z= 0.186 Angle : 0.654 8.488 15412 Z= 0.318 Chirality : 0.042 0.184 1726 Planarity : 0.005 0.042 1978 Dihedral : 4.762 31.633 1528 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.47 % Favored : 91.39 % Rotamer: Outliers : 3.31 % Allowed : 18.39 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.34 (0.24), residues: 1382 helix: 3.09 (0.24), residues: 486 sheet: 0.02 (0.32), residues: 264 loop : -2.16 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 400 HIS 0.006 0.001 HIS B 532 PHE 0.013 0.001 PHE B 265 TYR 0.010 0.001 TYR B 423 ARG 0.004 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.396 Fit side-chains REVERT: A 362 ILE cc_start: 0.9100 (mt) cc_final: 0.8776 (tt) REVERT: B 109 MET cc_start: 0.2275 (OUTLIER) cc_final: 0.1466 (tmm) REVERT: B 174 HIS cc_start: 0.7207 (t70) cc_final: 0.6951 (t70) REVERT: B 185 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7173 (t0) REVERT: B 309 GLN cc_start: 0.8634 (pm20) cc_final: 0.8336 (pm20) REVERT: B 512 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7596 (ttt90) REVERT: B 557 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8703 (tp30) REVERT: B 649 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7650 (pp) REVERT: D 362 ILE cc_start: 0.9084 (mt) cc_final: 0.8781 (tt) REVERT: E 109 MET cc_start: 0.4282 (mtm) cc_final: 0.3221 (tmm) REVERT: E 131 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7704 (pp) REVERT: E 306 ASP cc_start: 0.8577 (t0) cc_final: 0.8343 (t0) REVERT: E 309 GLN cc_start: 0.8552 (pm20) cc_final: 0.8311 (pm20) REVERT: E 512 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7605 (ttt90) REVERT: E 557 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8865 (tp30) REVERT: E 649 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7655 (pp) outliers start: 39 outliers final: 26 residues processed: 218 average time/residue: 0.2108 time to fit residues: 71.3894 Evaluate side-chains 227 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11296 Z= 0.235 Angle : 0.683 9.668 15412 Z= 0.331 Chirality : 0.043 0.178 1726 Planarity : 0.006 0.042 1978 Dihedral : 4.777 32.741 1528 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.97 % Favored : 90.88 % Rotamer: Outliers : 2.88 % Allowed : 18.90 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.30 (0.24), residues: 1382 helix: 3.01 (0.24), residues: 488 sheet: -0.07 (0.31), residues: 264 loop : -2.12 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 171 HIS 0.005 0.001 HIS B 532 PHE 0.013 0.002 PHE E 265 TYR 0.009 0.001 TYR E 423 ARG 0.004 0.000 ARG A 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.478 Fit side-chains REVERT: A 362 ILE cc_start: 0.9127 (mt) cc_final: 0.8794 (tt) REVERT: B 109 MET cc_start: 0.2201 (OUTLIER) cc_final: 0.1527 (tmm) REVERT: B 185 ASN cc_start: 0.7725 (m110) cc_final: 0.7203 (t0) REVERT: B 309 GLN cc_start: 0.8648 (pm20) cc_final: 0.8343 (pm20) REVERT: B 512 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (ttt90) REVERT: B 557 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8716 (tp30) REVERT: B 649 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7649 (pp) REVERT: D 362 ILE cc_start: 0.9095 (mt) cc_final: 0.8793 (tt) REVERT: E 109 MET cc_start: 0.4186 (mtm) cc_final: 0.3261 (tmm) REVERT: E 131 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7694 (pp) REVERT: E 306 ASP cc_start: 0.8520 (t0) cc_final: 0.8277 (t0) REVERT: E 309 GLN cc_start: 0.8568 (pm20) cc_final: 0.8317 (pm20) REVERT: E 512 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7609 (ttt90) REVERT: E 557 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8872 (tp30) REVERT: E 649 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7738 (pp) outliers start: 34 outliers final: 26 residues processed: 218 average time/residue: 0.1826 time to fit residues: 60.7251 Evaluate side-chains 226 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 46 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.101947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081989 restraints weight = 19116.047| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.22 r_work: 0.3005 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11296 Z= 0.201 Angle : 0.664 8.518 15412 Z= 0.323 Chirality : 0.042 0.172 1726 Planarity : 0.006 0.041 1978 Dihedral : 4.743 31.989 1528 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 3.05 % Allowed : 18.64 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.37 (0.24), residues: 1382 helix: 3.05 (0.24), residues: 488 sheet: 0.00 (0.31), residues: 264 loop : -2.07 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.005 0.001 HIS E 532 PHE 0.013 0.001 PHE B 265 TYR 0.010 0.001 TYR E 423 ARG 0.004 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.46 seconds wall clock time: 44 minutes 6.18 seconds (2646.18 seconds total)