Starting phenix.real_space_refine on Fri Sep 27 08:57:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/09_2024/7k6q_22692.cif" } resolution = 3.1 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= 0.004 sd= 1.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 34 5.16 5 C 8919 2.51 5 N 2846 2.21 5 O 3487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 15578 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 719 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2, 'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3029 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 485 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 9.37, per 1000 atoms: 0.60 Number of scatterers: 15578 At special positions: 0 Unit cell: (110.745, 113.85, 124.2, 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) S 34 16.00 P 292 15.00 O 3487 8.00 N 2846 7.00 C 8919 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: 3.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2318 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 60.4% alpha, 6.0% beta 142 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 7.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.463A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.666A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.533A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.550A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.518A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 195 through 202 Processing helix chain 'K' and resid 211 through 215 Processing helix chain 'K' and resid 263 through 278 Processing helix chain 'K' and resid 283 through 303 removed outlier: 3.557A pdb=" N ILE K 292 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU K 293 " --> pdb=" O LYS K 289 " (cutoff:3.500A) Proline residue: K 294 - end of helix Processing helix chain 'K' and resid 304 through 321 removed outlier: 3.683A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 334 removed outlier: 3.646A pdb=" N ILE K 327 " --> pdb=" O PRO K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 354 removed outlier: 3.830A pdb=" N HIS K 343 " --> pdb=" O ARG K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 364 removed outlier: 5.886A pdb=" N ASN K 359 " --> pdb=" O PRO K 356 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS K 363 " --> pdb=" O LYS K 360 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR K 364 " --> pdb=" O LEU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 387 Processing helix chain 'K' and resid 403 through 413 Processing helix chain 'K' and resid 424 through 446 Processing helix chain 'K' and resid 463 through 470 Processing helix chain 'K' and resid 484 through 496 Processing helix chain 'K' and resid 525 through 527 No H-bonds generated for 'chain 'K' and resid 525 through 527' Processing helix chain 'K' and resid 565 through 570 removed outlier: 3.771A pdb=" N ARG K 569 " --> pdb=" O SER K 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.582A pdb=" N TYR L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.306A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.670A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.887A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.601A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 186 through 188 Processing sheet with id=AB1, first strand: chain 'K' and resid 237 through 240 Processing sheet with id=AB2, first strand: chain 'K' and resid 452 through 455 removed outlier: 6.198A pdb=" N SER K 418 " --> pdb=" O GLU K 453 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER K 455 " --> pdb=" O SER K 418 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY K 420 " --> pdb=" O SER K 455 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE K 395 " --> pdb=" O PHE K 419 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS K 421 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP K 397 " --> pdb=" O CYS K 421 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR K 394 " --> pdb=" O VAL K 475 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU K 477 " --> pdb=" O THR K 394 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET K 396 " --> pdb=" O LEU K 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 15 removed outlier: 6.588A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2978 1.33 - 1.45: 5034 1.45 - 1.57: 7807 1.57 - 1.69: 580 1.69 - 1.81: 55 Bond restraints: 16454 Sorted by residual: bond pdb=" O3' DA I 91 " pdb=" P DC I 92 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" N ASP D 51 " pdb=" CA ASP D 51 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.53e+00 bond pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.23e-02 6.61e+03 7.24e+00 ... (remaining 16449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 22466 1.75 - 3.50: 911 3.50 - 5.25: 118 5.25 - 7.00: 21 7.00 - 8.75: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " pdb=" O3' DA I 91 " ideal model delta sigma weight residual 110.00 103.65 6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' DT J 15 " pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 111.50 117.75 -6.25 1.50e+00 4.44e-01 1.74e+01 angle pdb=" O3' DA I 90 " pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 111.50 105.33 6.17 1.50e+00 4.44e-01 1.69e+01 angle pdb=" O3' DT I 89 " pdb=" C3' DT I 89 " pdb=" C2' DT I 89 " ideal model delta sigma weight residual 111.50 106.14 5.36 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 110.00 104.64 5.36 1.50e+00 4.44e-01 1.28e+01 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 7471 29.40 - 58.81: 1574 58.81 - 88.21: 93 88.21 - 117.62: 1 117.62 - 147.02: 3 Dihedral angle restraints: 9142 sinusoidal: 5555 harmonic: 3587 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 72.98 147.02 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 73.40 146.60 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 86.16 133.84 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 9139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2363 0.064 - 0.128: 319 0.128 - 0.192: 19 0.192 - 0.256: 3 0.256 - 0.320: 1 Chirality restraints: 2705 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2' SAM K 601 " pdb=" C1' SAM K 601 " pdb=" C3' SAM K 601 " pdb=" O2' SAM K 601 " both_signs ideal model delta sigma weight residual False -2.76 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DT I 89 " pdb=" C4' DT I 89 " pdb=" O3' DT I 89 " pdb=" C2' DT I 89 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2702 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 86 " -0.219 9.50e-02 1.11e+02 9.83e-02 6.51e+00 pdb=" NE ARG H 86 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 86 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 86 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 86 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 42 " -0.203 9.50e-02 1.11e+02 9.15e-02 6.12e+00 pdb=" NE ARG E 42 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 42 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 42 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 42 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO H 103 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.031 5.00e-02 4.00e+02 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 439 2.67 - 3.23: 13564 3.23 - 3.78: 29161 3.78 - 4.34: 37776 4.34 - 4.90: 55653 Nonbonded interactions: 136593 Sorted by model distance: nonbonded pdb=" OE2 GLU K 422 " pdb=" O2' SAM K 601 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR H 32 " pdb=" OP1 DC J 104 " model vdw 2.114 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR K 274 " pdb=" OD2 ASP K 344 " model vdw 2.183 3.040 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 83 " model vdw 2.214 3.120 ... (remaining 136588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 19 or (resid 20 and (name N or name CA or nam \ e C or name O or name CB )) or resid 21 through 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 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: 2.480 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.006 0.061 16454 Z= 0.312 Angle : 0.777 8.745 23521 Z= 0.457 Chirality : 0.042 0.320 2705 Planarity : 0.006 0.098 1971 Dihedral : 24.803 147.020 6824 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.37 (0.24), residues: 1201 helix: 1.64 (0.19), residues: 717 sheet: -0.22 (0.56), residues: 85 loop : -0.07 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 543 HIS 0.010 0.001 HIS K 355 PHE 0.014 0.001 PHE G 25 TYR 0.011 0.001 TYR D 40 ARG 0.018 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.308 Fit side-chains REVERT: B 20 LYS cc_start: 0.8441 (tttm) cc_final: 0.7988 (ttmt) REVERT: B 25 ASN cc_start: 0.8207 (m-40) cc_final: 0.7936 (m-40) REVERT: D 119 THR cc_start: 0.8678 (m) cc_final: 0.8443 (p) REVERT: E 42 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7326 (mtt180) REVERT: E 59 GLU cc_start: 0.8132 (pm20) cc_final: 0.7785 (pm20) REVERT: E 74 ILE cc_start: 0.9059 (mm) cc_final: 0.8830 (mt) REVERT: F 77 LYS cc_start: 0.8813 (mttt) cc_final: 0.8419 (mtmt) REVERT: F 84 MET cc_start: 0.8239 (mmm) cc_final: 0.8010 (mmm) REVERT: H 51 ASP cc_start: 0.7563 (p0) cc_final: 0.7319 (p0) REVERT: K 493 LYS cc_start: 0.8665 (tttt) cc_final: 0.8426 (ttmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3632 time to fit residues: 86.1733 Evaluate side-chains 135 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 93 GLN B 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS K 355 HIS K 521 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16454 Z= 0.251 Angle : 0.560 5.861 23521 Z= 0.328 Chirality : 0.037 0.156 2705 Planarity : 0.004 0.052 1971 Dihedral : 28.765 140.166 4590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.61 % Allowed : 5.85 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.76 (0.24), residues: 1201 helix: 1.95 (0.19), residues: 726 sheet: 0.06 (0.58), residues: 85 loop : 0.01 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.005 0.001 HIS K 347 PHE 0.016 0.002 PHE G 25 TYR 0.013 0.001 TYR C 57 ARG 0.008 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9271 (p) cc_final: 0.9050 (p) REVERT: A 59 GLU cc_start: 0.7730 (pm20) cc_final: 0.7385 (pm20) REVERT: A 123 ASP cc_start: 0.8754 (m-30) cc_final: 0.8502 (m-30) REVERT: B 20 LYS cc_start: 0.8478 (tttm) cc_final: 0.8047 (ttmt) REVERT: B 85 ASP cc_start: 0.8438 (m-30) cc_final: 0.8238 (m-30) REVERT: E 59 GLU cc_start: 0.8057 (pm20) cc_final: 0.7519 (pm20) REVERT: F 77 LYS cc_start: 0.8836 (mttt) cc_final: 0.8440 (mtmt) REVERT: F 92 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7772 (ttp80) REVERT: H 51 ASP cc_start: 0.7718 (p0) cc_final: 0.7493 (p0) REVERT: H 59 MET cc_start: 0.8372 (tpp) cc_final: 0.8168 (tpp) REVERT: K 445 TYR cc_start: 0.7340 (m-80) cc_final: 0.7049 (m-10) REVERT: K 493 LYS cc_start: 0.8640 (tttt) cc_final: 0.8420 (ttmm) outliers start: 6 outliers final: 6 residues processed: 149 average time/residue: 0.3316 time to fit residues: 69.6291 Evaluate side-chains 142 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 68 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16454 Z= 0.217 Angle : 0.528 5.707 23521 Z= 0.312 Chirality : 0.036 0.144 2705 Planarity : 0.004 0.049 1971 Dihedral : 28.839 140.303 4590 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.99 (0.24), residues: 1201 helix: 2.15 (0.19), residues: 726 sheet: 0.07 (0.58), residues: 85 loop : 0.09 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.008 0.001 HIS K 202 PHE 0.014 0.001 PHE G 25 TYR 0.013 0.001 TYR C 57 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.328 Fit side-chains REVERT: A 58 THR cc_start: 0.9277 (p) cc_final: 0.9070 (p) REVERT: A 123 ASP cc_start: 0.8815 (m-30) cc_final: 0.8469 (m-30) REVERT: B 85 ASP cc_start: 0.8307 (m-30) cc_final: 0.8060 (m-30) REVERT: E 59 GLU cc_start: 0.7924 (pm20) cc_final: 0.7431 (pm20) REVERT: F 92 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7841 (ttp80) REVERT: H 51 ASP cc_start: 0.7692 (p0) cc_final: 0.7455 (p0) REVERT: H 59 MET cc_start: 0.8416 (tpp) cc_final: 0.8171 (tpp) REVERT: K 445 TYR cc_start: 0.7459 (m-80) cc_final: 0.7130 (m-10) REVERT: K 493 LYS cc_start: 0.8660 (tttt) cc_final: 0.8455 (ttmm) REVERT: K 540 SER cc_start: 0.8828 (t) cc_final: 0.8505 (m) outliers start: 10 outliers final: 6 residues processed: 146 average time/residue: 0.3147 time to fit residues: 65.4972 Evaluate side-chains 141 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16454 Z= 0.239 Angle : 0.537 7.374 23521 Z= 0.314 Chirality : 0.036 0.146 2705 Planarity : 0.004 0.046 1971 Dihedral : 28.939 139.386 4590 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.41 % Allowed : 9.08 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.07 (0.24), residues: 1201 helix: 2.21 (0.19), residues: 726 sheet: 0.14 (0.59), residues: 85 loop : 0.13 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.011 0.001 HIS K 202 PHE 0.016 0.002 PHE G 25 TYR 0.012 0.001 TYR C 57 ARG 0.009 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.306 Fit side-chains REVERT: A 58 THR cc_start: 0.9306 (p) cc_final: 0.9091 (p) REVERT: A 59 GLU cc_start: 0.7742 (pm20) cc_final: 0.7412 (pm20) REVERT: A 123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8509 (m-30) REVERT: B 20 LYS cc_start: 0.8555 (tttm) cc_final: 0.8088 (ttmt) REVERT: E 59 GLU cc_start: 0.7953 (pm20) cc_final: 0.7407 (pm20) REVERT: E 120 MET cc_start: 0.7896 (mtp) cc_final: 0.7499 (mtt) REVERT: E 123 ASP cc_start: 0.7925 (m-30) cc_final: 0.7716 (m-30) REVERT: G 90 ASP cc_start: 0.8221 (t0) cc_final: 0.7962 (t0) REVERT: H 59 MET cc_start: 0.8446 (tpp) cc_final: 0.8180 (tpp) REVERT: K 380 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7258 (mp) REVERT: K 397 ASP cc_start: 0.8310 (t0) cc_final: 0.8106 (t0) REVERT: K 493 LYS cc_start: 0.8657 (tttt) cc_final: 0.8444 (ttmm) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.3130 time to fit residues: 63.8670 Evaluate side-chains 147 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16454 Z= 0.222 Angle : 0.523 7.343 23521 Z= 0.308 Chirality : 0.035 0.147 2705 Planarity : 0.004 0.047 1971 Dihedral : 28.909 138.544 4590 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.41 % Allowed : 9.89 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.13 (0.24), residues: 1201 helix: 2.26 (0.19), residues: 726 sheet: 0.19 (0.59), residues: 85 loop : 0.15 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE G 25 TYR 0.013 0.001 TYR C 57 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.410 Fit side-chains REVERT: A 58 THR cc_start: 0.9294 (p) cc_final: 0.9087 (p) REVERT: A 123 ASP cc_start: 0.8781 (m-30) cc_final: 0.8512 (m-30) REVERT: B 20 LYS cc_start: 0.8549 (tttm) cc_final: 0.8101 (ttmt) REVERT: C 94 ASN cc_start: 0.9101 (t0) cc_final: 0.8765 (t0) REVERT: E 59 GLU cc_start: 0.7925 (pm20) cc_final: 0.7370 (pm20) REVERT: E 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7584 (mtt) REVERT: G 90 ASP cc_start: 0.8238 (t0) cc_final: 0.7957 (t0) REVERT: H 59 MET cc_start: 0.8416 (tpp) cc_final: 0.8144 (tpp) REVERT: K 380 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7261 (mp) REVERT: K 397 ASP cc_start: 0.8285 (t0) cc_final: 0.8059 (t0) REVERT: K 493 LYS cc_start: 0.8678 (tttt) cc_final: 0.8453 (ttmm) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.3222 time to fit residues: 66.6302 Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16454 Z= 0.211 Angle : 0.519 7.803 23521 Z= 0.306 Chirality : 0.035 0.146 2705 Planarity : 0.004 0.044 1971 Dihedral : 28.887 138.169 4590 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.51 % Allowed : 10.70 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.18 (0.24), residues: 1201 helix: 2.30 (0.19), residues: 726 sheet: 0.28 (0.60), residues: 85 loop : 0.14 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 PHE 0.011 0.001 PHE G 25 TYR 0.012 0.001 TYR C 57 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.363 Fit side-chains REVERT: A 58 THR cc_start: 0.9288 (p) cc_final: 0.9085 (p) REVERT: A 59 GLU cc_start: 0.7653 (pm20) cc_final: 0.7450 (pm20) REVERT: A 123 ASP cc_start: 0.8764 (m-30) cc_final: 0.8514 (m-30) REVERT: C 94 ASN cc_start: 0.9100 (t0) cc_final: 0.8768 (t0) REVERT: E 59 GLU cc_start: 0.7881 (pm20) cc_final: 0.7321 (pm20) REVERT: E 120 MET cc_start: 0.8056 (mtp) cc_final: 0.7665 (mtt) REVERT: G 90 ASP cc_start: 0.8190 (t0) cc_final: 0.7906 (t0) REVERT: H 59 MET cc_start: 0.8420 (tpp) cc_final: 0.8133 (tpp) REVERT: K 380 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7236 (mp) REVERT: K 397 ASP cc_start: 0.8262 (t0) cc_final: 0.8023 (t0) REVERT: K 493 LYS cc_start: 0.8689 (tttt) cc_final: 0.8463 (ttmm) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 0.3097 time to fit residues: 66.0710 Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16454 Z= 0.270 Angle : 0.548 8.486 23521 Z= 0.318 Chirality : 0.036 0.147 2705 Planarity : 0.004 0.046 1971 Dihedral : 29.085 137.872 4590 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.31 % Allowed : 11.60 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.07 (0.24), residues: 1201 helix: 2.24 (0.19), residues: 726 sheet: 0.27 (0.60), residues: 85 loop : 0.03 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.006 0.001 HIS K 347 PHE 0.014 0.002 PHE G 25 TYR 0.024 0.002 TYR D 83 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.199 Fit side-chains REVERT: A 58 THR cc_start: 0.9312 (p) cc_final: 0.9081 (p) REVERT: A 59 GLU cc_start: 0.7782 (pm20) cc_final: 0.7479 (pm20) REVERT: C 94 ASN cc_start: 0.9115 (t0) cc_final: 0.8778 (t0) REVERT: E 59 GLU cc_start: 0.7924 (pm20) cc_final: 0.7507 (pm20) REVERT: E 120 MET cc_start: 0.8074 (mtp) cc_final: 0.7573 (mtt) REVERT: G 90 ASP cc_start: 0.8264 (t0) cc_final: 0.7970 (t0) REVERT: H 59 MET cc_start: 0.8442 (tpp) cc_final: 0.8163 (tpp) REVERT: K 318 MET cc_start: 0.8077 (ppp) cc_final: 0.7781 (ppp) REVERT: K 380 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7234 (mp) REVERT: K 397 ASP cc_start: 0.8312 (t0) cc_final: 0.8000 (t0) REVERT: K 493 LYS cc_start: 0.8706 (tttt) cc_final: 0.8460 (ttmm) outliers start: 13 outliers final: 10 residues processed: 147 average time/residue: 0.3220 time to fit residues: 66.7971 Evaluate side-chains 150 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16454 Z= 0.348 Angle : 0.582 8.669 23521 Z= 0.335 Chirality : 0.038 0.150 2705 Planarity : 0.004 0.045 1971 Dihedral : 29.442 137.884 4590 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.51 % Allowed : 11.81 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.86 (0.24), residues: 1201 helix: 2.08 (0.19), residues: 726 sheet: 0.25 (0.60), residues: 83 loop : -0.09 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.006 0.001 HIS K 347 PHE 0.017 0.002 PHE E 84 TYR 0.012 0.002 TYR G 57 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.499 Fit side-chains REVERT: A 58 THR cc_start: 0.9353 (p) cc_final: 0.9114 (p) REVERT: A 59 GLU cc_start: 0.7755 (pm20) cc_final: 0.7410 (pm20) REVERT: E 59 GLU cc_start: 0.8011 (pm20) cc_final: 0.7578 (pm20) REVERT: E 77 ASP cc_start: 0.8276 (m-30) cc_final: 0.8042 (m-30) REVERT: E 120 MET cc_start: 0.8101 (mtp) cc_final: 0.7633 (mtt) REVERT: G 90 ASP cc_start: 0.8231 (t0) cc_final: 0.7952 (t0) REVERT: H 42 TYR cc_start: 0.7643 (t80) cc_final: 0.7315 (t80) REVERT: K 318 MET cc_start: 0.8176 (ppp) cc_final: 0.7818 (ppp) REVERT: K 380 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7387 (mp) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.3352 time to fit residues: 72.5082 Evaluate side-chains 151 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 131 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 93 GLN L 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16454 Z= 0.186 Angle : 0.526 8.968 23521 Z= 0.308 Chirality : 0.034 0.145 2705 Planarity : 0.004 0.043 1971 Dihedral : 28.910 138.449 4590 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.21 % Allowed : 12.01 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.15 (0.24), residues: 1201 helix: 2.32 (0.19), residues: 726 sheet: 0.55 (0.61), residues: 82 loop : -0.05 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR C 57 ARG 0.009 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8917 (m-30) cc_final: 0.8589 (m-30) REVERT: A 129 ARG cc_start: 0.8253 (tpt90) cc_final: 0.7746 (tpt170) REVERT: C 94 ASN cc_start: 0.9132 (t0) cc_final: 0.8808 (t0) REVERT: E 59 GLU cc_start: 0.7861 (pm20) cc_final: 0.7329 (pm20) REVERT: E 77 ASP cc_start: 0.8257 (m-30) cc_final: 0.8024 (m-30) REVERT: E 120 MET cc_start: 0.7993 (mtp) cc_final: 0.7698 (mtt) REVERT: G 90 ASP cc_start: 0.8178 (t0) cc_final: 0.7882 (t0) REVERT: H 42 TYR cc_start: 0.7551 (t80) cc_final: 0.7259 (t80) REVERT: K 318 MET cc_start: 0.8200 (ppp) cc_final: 0.7829 (ppp) REVERT: K 380 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7125 (mp) REVERT: K 397 ASP cc_start: 0.8156 (t0) cc_final: 0.7928 (t0) REVERT: L 72 ARG cc_start: 0.6554 (tmm-80) cc_final: 0.6109 (tmm-80) outliers start: 12 outliers final: 8 residues processed: 149 average time/residue: 0.3297 time to fit residues: 69.0794 Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16454 Z= 0.214 Angle : 0.538 9.287 23521 Z= 0.312 Chirality : 0.035 0.145 2705 Planarity : 0.004 0.046 1971 Dihedral : 28.994 138.317 4590 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.11 % Allowed : 12.21 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.14 (0.24), residues: 1201 helix: 2.33 (0.19), residues: 726 sheet: 0.49 (0.60), residues: 82 loop : -0.06 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 PHE 0.011 0.001 PHE E 84 TYR 0.013 0.001 TYR C 57 ARG 0.009 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 2.256 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8912 (m-30) cc_final: 0.8624 (m-30) REVERT: C 94 ASN cc_start: 0.9133 (t0) cc_final: 0.8801 (t0) REVERT: E 59 GLU cc_start: 0.7888 (pm20) cc_final: 0.7349 (pm20) REVERT: E 77 ASP cc_start: 0.8265 (m-30) cc_final: 0.8016 (m-30) REVERT: E 120 MET cc_start: 0.8018 (mtp) cc_final: 0.7581 (mtt) REVERT: G 90 ASP cc_start: 0.8198 (t0) cc_final: 0.7894 (t0) REVERT: H 59 MET cc_start: 0.8546 (tpp) cc_final: 0.8287 (tpp) REVERT: K 380 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7171 (mp) REVERT: K 397 ASP cc_start: 0.8071 (t0) cc_final: 0.7809 (t0) REVERT: L 7 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7362 (t) REVERT: L 72 ARG cc_start: 0.6621 (tmm-80) cc_final: 0.6174 (tmm-80) outliers start: 11 outliers final: 8 residues processed: 148 average time/residue: 0.3252 time to fit residues: 68.0674 Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain L residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080646 restraints weight = 27511.263| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3086 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16454 Z= 0.204 Angle : 0.538 9.392 23521 Z= 0.311 Chirality : 0.035 0.146 2705 Planarity : 0.004 0.045 1971 Dihedral : 28.951 138.495 4590 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.11 % Allowed : 12.51 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.14 (0.24), residues: 1201 helix: 2.31 (0.19), residues: 726 sheet: 0.51 (0.61), residues: 83 loop : -0.05 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 PHE 0.011 0.001 PHE E 84 TYR 0.013 0.001 TYR C 57 ARG 0.009 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.05 seconds wall clock time: 51 minutes 26.24 seconds (3086.24 seconds total)