Starting phenix.real_space_refine on Tue Feb 20 23:20:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2024/7oi0_12916.pdb" } resolution = 2.76 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= 0.007 sd= 0.083 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 963 5.49 5 S 30 5.16 5 C 14335 2.51 5 N 5400 2.21 5 O 8527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 14": "OE1" <-> "OE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29255 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 702 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "A" Number of atoms: 20700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 20700 Classifications: {'RNA': 963} Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 44, 'rna3p_pur': 487, 'rna3p_pyr': 358} Link IDs: {'rna2p': 118, 'rna3p': 844} Chain breaks: 2 Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 337 Classifications: {'water': 337} Link IDs: {None: 336} Time building chain proxies: 15.31, per 1000 atoms: 0.52 Number of scatterers: 29255 At special positions: 0 Unit cell: (111.8, 155.66, 212.42, 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 30 16.00 P 963 15.00 O 8527 8.00 N 5400 7.00 C 14335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1930 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.9% alpha, 15.9% beta 338 base pairs and 532 stacking pairs defined. Time for finding SS restraints: 15.87 Creating SS restraints... Processing helix chain 'D' and resid 6 through 14 removed outlier: 3.928A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.603A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 4.030A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.640A pdb=" N LYS F 53 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 54 " --> pdb=" O ILE F 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 50 through 54' Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.153A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.694A pdb=" N MET H 9 " --> pdb=" O PRO H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'K' and resid 58 through 72 Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 23 through 46 removed outlier: 4.111A pdb=" N ALA O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 removed outlier: 3.678A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 5.012A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.845A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'R' and resid 25 through 32 removed outlier: 3.662A pdb=" N LYS R 29 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN R 30 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 3 through 39 Processing helix chain 'T' and resid 42 through 63 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 67 through 86 Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.736A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 61 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.900A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 40 through 45 removed outlier: 6.645A pdb=" N ILE K 33 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP K 43 " --> pdb=" O VAL K 31 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL K 31 " --> pdb=" O TRP K 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 28 through 31 removed outlier: 10.174A pdb=" N VAL L 92 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR L 63 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR L 94 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 50 through 51 removed outlier: 4.865A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 7 through 16 removed outlier: 7.901A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP Q 14 " --> pdb=" O SER Q 19 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER Q 19 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 15.667A pdb=" N LYS Q 70 " --> pdb=" O THR Q 40 " (cutoff:3.500A) removed outlier: 14.072A pdb=" N LYS Q 42 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N TRP Q 72 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS Q 44 " --> pdb=" O TRP Q 72 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU Q 74 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N HIS Q 46 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG Q 76 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 840 hydrogen bonds 1286 hydrogen bond angles 0 basepair planarities 338 basepair parallelities 532 stacking parallelities Total time for adding SS restraints: 25.28 Time building geometry restraints manager: 19.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2788 1.30 - 1.43: 14063 1.43 - 1.56: 12652 1.56 - 1.68: 1924 1.68 - 1.81: 51 Bond restraints: 31478 Sorted by residual: bond pdb=" CB VAL P 20 " pdb=" CG2 VAL P 20 " ideal model delta sigma weight residual 1.521 1.404 0.117 3.30e-02 9.18e+02 1.25e+01 bond pdb=" C5 G A 108 " pdb=" C6 G A 108 " ideal model delta sigma weight residual 1.419 1.350 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE T 66 " pdb=" CA ILE T 66 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N9 A A 452 " pdb=" C4 A A 452 " ideal model delta sigma weight residual 1.374 1.310 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CD2 HIS P 9 " pdb=" NE2 HIS P 9 " ideal model delta sigma weight residual 1.374 1.339 0.035 1.10e-02 8.26e+03 9.97e+00 ... (remaining 31473 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.80: 4486 104.80 - 112.92: 18953 112.92 - 121.04: 14899 121.04 - 129.16: 7869 129.16 - 137.28: 1089 Bond angle restraints: 47296 Sorted by residual: angle pdb=" C4' G A 416 " pdb=" C3' G A 416 " pdb=" O3' G A 416 " ideal model delta sigma weight residual 113.00 125.61 -12.61 1.50e+00 4.44e-01 7.07e+01 angle pdb=" O2' G A 416 " pdb=" C2' G A 416 " pdb=" C1' G A 416 " ideal model delta sigma weight residual 108.40 97.74 10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C4' A A 465 " pdb=" C3' A A 465 " pdb=" O3' A A 465 " ideal model delta sigma weight residual 113.00 123.41 -10.41 1.50e+00 4.44e-01 4.82e+01 angle pdb=" C4' A A 415 " pdb=" C3' A A 415 " pdb=" O3' A A 415 " ideal model delta sigma weight residual 113.00 121.46 -8.46 1.50e+00 4.44e-01 3.18e+01 angle pdb=" O4' A A 182 " pdb=" C1' A A 182 " pdb=" N9 A A 182 " ideal model delta sigma weight residual 108.20 116.16 -7.96 1.50e+00 4.44e-01 2.82e+01 ... (remaining 47291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 17480 35.35 - 70.70: 2452 70.70 - 106.05: 275 106.05 - 141.39: 7 141.39 - 176.74: 11 Dihedral angle restraints: 20225 sinusoidal: 17239 harmonic: 2986 Sorted by residual: dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual -160.00 5.95 -165.95 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 50.65 149.35 1 1.50e+01 4.44e-03 7.94e+01 ... (remaining 20222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5788 0.138 - 0.275: 254 0.275 - 0.413: 13 0.413 - 0.551: 0 0.551 - 0.689: 1 Chirality restraints: 6056 Sorted by residual: chirality pdb=" C3' A A 465 " pdb=" C4' A A 465 " pdb=" O3' A A 465 " pdb=" C2' A A 465 " both_signs ideal model delta sigma weight residual False -2.48 -1.79 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CB VAL P 20 " pdb=" CA VAL P 20 " pdb=" CG1 VAL P 20 " pdb=" CG2 VAL P 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE L 66 " pdb=" CA ILE L 66 " pdb=" CG1 ILE L 66 " pdb=" CG2 ILE L 66 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 6053 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 335 " -0.069 2.00e-02 2.50e+03 3.65e-02 3.00e+01 pdb=" N1 C A 335 " 0.080 2.00e-02 2.50e+03 pdb=" C2 C A 335 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C A 335 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C A 335 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C A 335 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 335 " -0.018 2.00e-02 2.50e+03 pdb=" C5 C A 335 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 335 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 181 " -0.069 2.00e-02 2.50e+03 3.16e-02 2.75e+01 pdb=" N9 A A 181 " 0.072 2.00e-02 2.50e+03 pdb=" C8 A A 181 " 0.012 2.00e-02 2.50e+03 pdb=" N7 A A 181 " -0.013 2.00e-02 2.50e+03 pdb=" C5 A A 181 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A 181 " -0.011 2.00e-02 2.50e+03 pdb=" N6 A A 181 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 181 " -0.014 2.00e-02 2.50e+03 pdb=" C2 A A 181 " 0.009 2.00e-02 2.50e+03 pdb=" N3 A A 181 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A A 181 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 438 " 0.064 2.00e-02 2.50e+03 3.21e-02 2.32e+01 pdb=" N1 U A 438 " -0.063 2.00e-02 2.50e+03 pdb=" C2 U A 438 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U A 438 " -0.009 2.00e-02 2.50e+03 pdb=" N3 U A 438 " 0.015 2.00e-02 2.50e+03 pdb=" C4 U A 438 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U A 438 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U A 438 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U A 438 " -0.020 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 729 2.56 - 3.15: 23322 3.15 - 3.73: 63512 3.73 - 4.32: 87681 4.32 - 4.90: 112427 Nonbonded interactions: 287671 Sorted by model distance: nonbonded pdb=" N2 G A 444 " pdb=" O2 C A 490 " model vdw 1.977 2.496 nonbonded pdb=" N2 G A 457 " pdb=" O2 C A 475 " model vdw 1.982 2.496 nonbonded pdb=" O6 G A 410 " pdb=" O2' U A 429 " model vdw 1.983 2.440 nonbonded pdb=" O2 C A 658 " pdb=" N2 G A 748 " model vdw 2.021 2.496 nonbonded pdb=" OD1 ASP D 98 " pdb=" N ASN D 99 " model vdw 2.025 2.520 ... (remaining 287666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.130 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 106.510 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.014 0.117 31478 Z= 0.836 Angle : 1.079 12.609 47296 Z= 0.566 Chirality : 0.063 0.689 6056 Planarity : 0.007 0.062 2401 Dihedral : 24.491 176.743 18295 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.24), residues: 1017 helix: -0.71 (0.26), residues: 379 sheet: -2.44 (0.38), residues: 147 loop : -2.14 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 72 HIS 0.013 0.002 HIS D 119 PHE 0.016 0.003 PHE P 39 TYR 0.027 0.003 TYR L 116 ARG 0.021 0.002 ARG P 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 115 average time/residue: 1.4880 time to fit residues: 199.8303 Evaluate side-chains 105 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain O residue 67 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 50.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31478 Z= 0.185 Angle : 0.625 11.189 47296 Z= 0.319 Chirality : 0.035 0.244 6056 Planarity : 0.005 0.055 2401 Dihedral : 24.645 177.454 16234 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.75 % Allowed : 10.49 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1017 helix: 0.59 (0.26), residues: 385 sheet: -2.04 (0.38), residues: 156 loop : -1.90 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 60 HIS 0.010 0.001 HIS O 41 PHE 0.011 0.001 PHE D 106 TYR 0.013 0.001 TYR F 59 ARG 0.007 0.001 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 125 average time/residue: 1.4108 time to fit residues: 207.6285 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 178 optimal weight: 50.0000 chunk 192 optimal weight: 50.0000 chunk 158 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 31478 Z= 0.336 Angle : 0.681 12.168 47296 Z= 0.344 Chirality : 0.039 0.270 6056 Planarity : 0.005 0.060 2401 Dihedral : 24.565 177.679 16230 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.68 % Allowed : 14.22 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.19 (0.26), residues: 1017 helix: 0.88 (0.26), residues: 380 sheet: -2.02 (0.38), residues: 169 loop : -1.72 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 72 HIS 0.018 0.002 HIS F 3 PHE 0.014 0.001 PHE D 106 TYR 0.016 0.002 TYR L 116 ARG 0.007 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 ASN cc_start: 0.8177 (m-40) cc_final: 0.7917 (m-40) REVERT: Q 39 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7324 (mmp-170) REVERT: Q 59 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6201 (mt-10) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 1.4764 time to fit residues: 202.8797 Evaluate side-chains 110 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN L 95 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31478 Z= 0.228 Angle : 0.599 11.795 47296 Z= 0.304 Chirality : 0.035 0.239 6056 Planarity : 0.005 0.050 2401 Dihedral : 24.358 177.828 16230 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.80 % Allowed : 15.85 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.97 (0.26), residues: 1017 helix: 1.12 (0.26), residues: 386 sheet: -1.99 (0.38), residues: 169 loop : -1.64 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 60 HIS 0.010 0.001 HIS O 41 PHE 0.013 0.001 PHE P 32 TYR 0.014 0.001 TYR D 75 ARG 0.009 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 ASN cc_start: 0.8087 (m-40) cc_final: 0.7778 (m-40) REVERT: Q 39 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7241 (mmp-170) outliers start: 24 outliers final: 8 residues processed: 121 average time/residue: 1.5091 time to fit residues: 214.4918 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 50.0000 chunk 47 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN D 151 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 31478 Z= 0.397 Angle : 0.702 12.584 47296 Z= 0.351 Chirality : 0.041 0.266 6056 Planarity : 0.005 0.040 2401 Dihedral : 24.430 177.440 16230 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.04 (0.26), residues: 1017 helix: 1.04 (0.26), residues: 380 sheet: -2.04 (0.40), residues: 154 loop : -1.65 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 72 HIS 0.011 0.001 HIS O 41 PHE 0.011 0.001 PHE P 32 TYR 0.019 0.002 TYR F 4 ARG 0.010 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 125 ASN cc_start: 0.8184 (m-40) cc_final: 0.7935 (m-40) REVERT: H 79 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7886 (ptm-80) REVERT: L 107 LYS cc_start: 0.6747 (mppt) cc_final: 0.6432 (mppt) REVERT: Q 39 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7379 (mmp-170) outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 1.4218 time to fit residues: 191.0725 Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN O 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31478 Z= 0.186 Angle : 0.589 15.465 47296 Z= 0.299 Chirality : 0.034 0.237 6056 Planarity : 0.004 0.045 2401 Dihedral : 24.285 177.654 16230 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.45 % Allowed : 17.95 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1017 helix: 1.32 (0.26), residues: 382 sheet: -1.99 (0.38), residues: 172 loop : -1.47 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 60 HIS 0.009 0.001 HIS O 41 PHE 0.009 0.001 PHE P 32 TYR 0.016 0.001 TYR D 75 ARG 0.012 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 39 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7236 (mmp-170) outliers start: 21 outliers final: 9 residues processed: 118 average time/residue: 1.3737 time to fit residues: 191.7097 Evaluate side-chains 109 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 0.0040 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN L 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 31478 Z= 0.402 Angle : 0.701 14.149 47296 Z= 0.350 Chirality : 0.041 0.270 6056 Planarity : 0.005 0.049 2401 Dihedral : 24.368 177.120 16230 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.91 % Allowed : 19.58 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.90 (0.26), residues: 1017 helix: 1.09 (0.26), residues: 383 sheet: -1.94 (0.40), residues: 154 loop : -1.54 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 72 HIS 0.007 0.001 HIS L 95 PHE 0.011 0.001 PHE P 32 TYR 0.017 0.002 TYR F 25 ARG 0.012 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8455 (mp) REVERT: D 125 ASN cc_start: 0.8165 (m-40) cc_final: 0.7858 (m-40) REVERT: H 79 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7885 (ptm-80) REVERT: P 5 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7774 (ptp-170) REVERT: Q 39 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7363 (mmp-170) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 1.4960 time to fit residues: 198.9397 Evaluate side-chains 117 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31478 Z= 0.225 Angle : 0.604 16.052 47296 Z= 0.305 Chirality : 0.035 0.241 6056 Planarity : 0.005 0.050 2401 Dihedral : 24.265 177.141 16230 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.15 % Allowed : 19.81 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.73 (0.27), residues: 1017 helix: 1.29 (0.26), residues: 383 sheet: -1.80 (0.39), residues: 172 loop : -1.46 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 72 HIS 0.008 0.001 HIS L 71 PHE 0.011 0.001 PHE P 32 TYR 0.022 0.001 TYR D 75 ARG 0.014 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8395 (mp) REVERT: D 125 ASN cc_start: 0.8088 (m-40) cc_final: 0.7730 (m-40) REVERT: P 4 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8957 (mm) REVERT: P 5 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7691 (ptp-170) REVERT: Q 39 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7320 (mmp-170) outliers start: 27 outliers final: 16 residues processed: 115 average time/residue: 1.4300 time to fit residues: 194.1600 Evaluate side-chains 114 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 30.0000 chunk 180 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 31478 Z= 0.538 Angle : 0.798 17.481 47296 Z= 0.393 Chirality : 0.046 0.303 6056 Planarity : 0.006 0.050 2401 Dihedral : 24.452 177.723 16230 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.50 % Allowed : 19.46 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.98 (0.26), residues: 1017 helix: 0.92 (0.26), residues: 383 sheet: -1.93 (0.39), residues: 160 loop : -1.49 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 72 HIS 0.006 0.001 HIS O 41 PHE 0.010 0.002 PHE P 38 TYR 0.020 0.002 TYR L 116 ARG 0.011 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 125 ASN cc_start: 0.8216 (m-40) cc_final: 0.7963 (m-40) REVERT: H 79 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7782 (ptm-80) REVERT: P 5 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7869 (ptp-170) REVERT: Q 39 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (mmp-170) outliers start: 30 outliers final: 18 residues processed: 114 average time/residue: 1.4855 time to fit residues: 199.5714 Evaluate side-chains 118 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 155 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.0470 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 31478 Z= 0.562 Angle : 0.874 59.195 47296 Z= 0.451 Chirality : 0.047 0.382 6056 Planarity : 0.006 0.049 2401 Dihedral : 24.453 177.726 16230 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.15 % Allowed : 20.28 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.99 (0.26), residues: 1017 helix: 0.90 (0.26), residues: 381 sheet: -1.93 (0.39), residues: 160 loop : -1.48 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 72 HIS 0.006 0.001 HIS P 9 PHE 0.010 0.002 PHE P 32 TYR 0.020 0.002 TYR L 116 ARG 0.018 0.001 ARG H 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8505 (mp) REVERT: D 125 ASN cc_start: 0.8217 (m-40) cc_final: 0.7964 (m-40) REVERT: H 79 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7784 (ptm-80) REVERT: P 5 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: Q 39 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7391 (mmp-170) outliers start: 27 outliers final: 18 residues processed: 113 average time/residue: 1.5004 time to fit residues: 198.6236 Evaluate side-chains 119 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 39 ARG Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.150063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122804 restraints weight = 48182.362| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.05 r_work: 0.3572 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 31478 Z= 0.562 Angle : 0.874 59.195 47296 Z= 0.451 Chirality : 0.047 0.382 6056 Planarity : 0.006 0.049 2401 Dihedral : 24.453 177.726 16230 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.56 % Allowed : 20.75 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.99 (0.26), residues: 1017 helix: 0.90 (0.26), residues: 381 sheet: -1.93 (0.39), residues: 160 loop : -1.48 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 72 HIS 0.006 0.001 HIS P 9 PHE 0.010 0.002 PHE P 32 TYR 0.020 0.002 TYR L 116 ARG 0.018 0.001 ARG H 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5622.97 seconds wall clock time: 104 minutes 21.73 seconds (6261.73 seconds total)