Starting phenix.real_space_refine on Sun Jul 21 21:54:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhg_36265/07_2024/8jhg_36265_neut.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1777 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 320 5.49 5 S 35 5.16 5 C 8303 2.51 5 N 2767 2.21 5 O 3403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 225": "OE1" <-> "OE2" Residue "K ASP 355": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14829 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2045 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 826 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 854 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3253 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3307 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1731 SG CYS K 319 83.419 30.899 85.584 1.00159.41 S ATOM 1746 SG CYS K 321 84.413 34.101 84.485 1.00163.58 S Time building chain proxies: 8.92, per 1000 atoms: 0.60 Number of scatterers: 14829 At special positions: 0 Unit cell: (110.4, 123.28, 141.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 320 15.00 O 3403 8.00 N 2767 7.00 C 8303 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: 7.25 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 59.5% alpha, 3.1% beta 130 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'K' and resid 77 through 89 Processing helix chain 'K' and resid 89 through 94 Processing helix chain 'K' and resid 140 through 147 removed outlier: 3.603A pdb=" N PHE K 144 " --> pdb=" O VAL K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 171 through 188 Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'K' and resid 356 through 361 Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.716A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.877A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.994A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.605A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.538A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.547A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.701A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.511A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.709A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.670A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.529A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.761A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.728A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.519A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.713A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.705A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.725A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.579A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.594A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.546A pdb=" N LYS G 127 " --> pdb=" O HIS G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.691A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.704A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 116 through 121 removed outlier: 4.041A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 196 through 199 removed outlier: 3.590A pdb=" N LEU K 198 " --> pdb=" O LYS K 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 231 through 233 removed outlier: 3.991A pdb=" N MET F 20 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.702A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.555A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.818A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.646A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 418 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 676 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 6.12 Time building geometry restraints manager: 7.58 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: 3140 1.33 - 1.45: 4873 1.45 - 1.57: 7043 1.57 - 1.69: 638 1.69 - 1.81: 55 Bond restraints: 15749 Sorted by residual: bond pdb=" N LEU K 351 " pdb=" CA LEU K 351 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.31e+00 bond pdb=" N THR K 354 " pdb=" CA THR K 354 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.33e-02 5.65e+03 8.84e+00 bond pdb=" N ARG K 352 " pdb=" CA ARG K 352 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.33e-02 5.65e+03 8.57e+00 bond pdb=" C2 SAM K 402 " pdb=" N3 SAM K 402 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" C8 SAM K 402 " pdb=" N7 SAM K 402 " ideal model delta sigma weight residual 1.298 1.353 -0.055 2.00e-02 2.50e+03 7.48e+00 ... (remaining 15744 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.71: 1659 105.71 - 112.82: 8671 112.82 - 119.94: 5680 119.94 - 127.06: 5882 127.06 - 134.17: 731 Bond angle restraints: 22623 Sorted by residual: angle pdb=" CA ARG K 352 " pdb=" C ARG K 352 " pdb=" O ARG K 352 " ideal model delta sigma weight residual 121.58 116.35 5.23 1.16e+00 7.43e-01 2.03e+01 angle pdb=" N ILE G 111 " pdb=" CA ILE G 111 " pdb=" C ILE G 111 " ideal model delta sigma weight residual 113.20 109.41 3.79 9.60e-01 1.09e+00 1.56e+01 angle pdb=" CA TRP K 218 " pdb=" C TRP K 218 " pdb=" O TRP K 218 " ideal model delta sigma weight residual 121.33 117.73 3.60 1.08e+00 8.57e-01 1.11e+01 angle pdb=" C ARG K 220 " pdb=" CA ARG K 220 " pdb=" CB ARG K 220 " ideal model delta sigma weight residual 116.54 112.82 3.72 1.15e+00 7.56e-01 1.05e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 113.18 108.92 4.26 1.33e+00 5.65e-01 1.03e+01 ... (remaining 22618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 7124 34.94 - 69.87: 1521 69.87 - 104.81: 19 104.81 - 139.74: 1 139.74 - 174.68: 3 Dihedral angle restraints: 8668 sinusoidal: 5654 harmonic: 3014 Sorted by residual: dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N MET F 20 " pdb=" CA MET F 20 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DT I 99 " pdb=" C3' DT I 99 " pdb=" O3' DT I 99 " pdb=" P DA I 100 " ideal model delta sinusoidal sigma weight residual -140.00 34.68 -174.68 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 138 " pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " pdb=" P DC J 139 " ideal model delta sinusoidal sigma weight residual 220.00 66.35 153.65 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1833 0.032 - 0.064: 547 0.064 - 0.096: 103 0.096 - 0.128: 57 0.128 - 0.160: 8 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C2' SAM K 402 " pdb=" C1' SAM K 402 " pdb=" C3' SAM K 402 " pdb=" O2' SAM K 402 " both_signs ideal model delta sigma weight residual False -2.76 -2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA LYS B 31 " pdb=" N LYS B 31 " pdb=" C LYS B 31 " pdb=" CB LYS B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" C1' DA J 161 " pdb=" O4' DA J 161 " pdb=" C2' DA J 161 " pdb=" N9 DA J 161 " both_signs ideal model delta sigma weight residual False 2.42 2.27 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2545 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG K 352 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ARG K 352 " 0.071 2.00e-02 2.50e+03 pdb=" O ARG K 352 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU K 353 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 198 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO K 199 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO K 199 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 199 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 161 " 0.021 2.00e-02 2.50e+03 1.33e-02 4.84e+00 pdb=" N9 DA J 161 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 161 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 161 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA J 161 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 161 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA J 161 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 161 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DA J 161 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DA J 161 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA J 161 " -0.004 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 590 2.70 - 3.25: 13135 3.25 - 3.80: 25464 3.80 - 4.35: 31687 4.35 - 4.90: 46568 Nonbonded interactions: 117444 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.152 2.440 nonbonded pdb=" OG SER K 255 " pdb=" O LYS K 258 " model vdw 2.171 2.440 nonbonded pdb=" O SER K 193 " pdb=" NZ LYS K 216 " model vdw 2.178 2.520 nonbonded pdb=" N2 DG J 159 " pdb=" O6 DG J 160 " model vdw 2.217 2.520 nonbonded pdb=" N3 DT I 7 " pdb=" O2 DT J 162 " model vdw 2.263 2.520 ... (remaining 117439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = (chain 'E' and ((resid 38 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 15 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 124)) } ncs_group { reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 122)) selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 50.840 Find NCS groups from input model: 0.400 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.004 0.058 15749 Z= 0.211 Angle : 0.590 9.152 22623 Z= 0.343 Chirality : 0.034 0.160 2548 Planarity : 0.004 0.055 1763 Dihedral : 26.864 174.678 6724 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.92 % Allowed : 0.58 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1019 helix: 1.78 (0.22), residues: 578 sheet: -2.95 (0.87), residues: 26 loop : -2.00 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 218 HIS 0.006 0.001 HIS K 245 PHE 0.008 0.001 PHE K 281 TYR 0.028 0.001 TYR F 88 ARG 0.003 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.230 Fit side-chains REVERT: K 100 MET cc_start: 0.7207 (pmm) cc_final: 0.6841 (pmm) REVERT: K 218 TRP cc_start: 0.5099 (OUTLIER) cc_final: 0.4635 (p90) REVERT: K 253 MET cc_start: 0.8311 (mtp) cc_final: 0.7931 (mmp) REVERT: K 294 LEU cc_start: 0.6562 (tp) cc_final: 0.5563 (tp) REVERT: F 88 TYR cc_start: 0.8973 (m-80) cc_final: 0.8549 (m-80) outliers start: 8 outliers final: 0 residues processed: 167 average time/residue: 0.2865 time to fit residues: 68.0306 Evaluate side-chains 140 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 218 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15749 Z= 0.225 Angle : 0.572 7.614 22623 Z= 0.332 Chirality : 0.035 0.151 2548 Planarity : 0.004 0.051 1763 Dihedral : 29.368 174.884 4680 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.15 % Allowed : 9.70 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1019 helix: 2.07 (0.22), residues: 590 sheet: -2.89 (0.90), residues: 26 loop : -2.09 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE K 183 TYR 0.018 0.001 TYR F 88 ARG 0.005 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.227 Fit side-chains REVERT: K 100 MET cc_start: 0.7172 (pmm) cc_final: 0.6788 (pmm) REVERT: K 218 TRP cc_start: 0.4978 (OUTLIER) cc_final: 0.4620 (p90) REVERT: K 253 MET cc_start: 0.8276 (mtp) cc_final: 0.7790 (mmp) REVERT: K 294 LEU cc_start: 0.6271 (tp) cc_final: 0.5003 (tp) REVERT: F 88 TYR cc_start: 0.8990 (m-80) cc_final: 0.8692 (m-80) REVERT: H 34 TYR cc_start: 0.8568 (m-80) cc_final: 0.8330 (m-80) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.2833 time to fit residues: 59.5472 Evaluate side-chains 147 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain H residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15749 Z= 0.170 Angle : 0.532 6.755 22623 Z= 0.311 Chirality : 0.033 0.151 2548 Planarity : 0.003 0.044 1763 Dihedral : 29.157 174.737 4680 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.15 % Allowed : 11.89 % Favored : 86.95 % 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: 1.02 (0.27), residues: 1019 helix: 2.45 (0.22), residues: 586 sheet: -2.86 (0.92), residues: 26 loop : -1.90 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE K 281 TYR 0.010 0.001 TYR F 88 ARG 0.006 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.102 Fit side-chains REVERT: K 100 MET cc_start: 0.7249 (pmm) cc_final: 0.6719 (pmm) REVERT: K 218 TRP cc_start: 0.5043 (OUTLIER) cc_final: 0.4657 (p90) REVERT: K 253 MET cc_start: 0.8201 (mtp) cc_final: 0.7864 (mmp) REVERT: K 294 LEU cc_start: 0.6355 (tp) cc_final: 0.5167 (tp) REVERT: A 113 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7731 (m170) REVERT: F 88 TYR cc_start: 0.8939 (m-80) cc_final: 0.8464 (m-80) outliers start: 10 outliers final: 6 residues processed: 154 average time/residue: 0.2574 time to fit residues: 57.8803 Evaluate side-chains 140 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15749 Z= 0.332 Angle : 0.622 8.223 22623 Z= 0.358 Chirality : 0.037 0.152 2548 Planarity : 0.004 0.054 1763 Dihedral : 29.452 174.335 4680 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.31 % Allowed : 13.39 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1019 helix: 2.03 (0.21), residues: 585 sheet: -2.86 (0.90), residues: 26 loop : -2.12 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 218 HIS 0.006 0.001 HIS D 46 PHE 0.012 0.001 PHE A 104 TYR 0.015 0.002 TYR C 57 ARG 0.004 0.000 ARG K 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.202 Fit side-chains REVERT: K 100 MET cc_start: 0.7215 (pmm) cc_final: 0.6852 (pmm) REVERT: K 218 TRP cc_start: 0.5202 (OUTLIER) cc_final: 0.4937 (p90) REVERT: K 253 MET cc_start: 0.8182 (mtp) cc_final: 0.7723 (mmp) REVERT: K 294 LEU cc_start: 0.6501 (tp) cc_final: 0.5366 (tp) REVERT: A 113 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7939 (m170) REVERT: D 97 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9040 (mp) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.2620 time to fit residues: 57.0016 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15749 Z= 0.190 Angle : 0.550 8.377 22623 Z= 0.320 Chirality : 0.033 0.157 2548 Planarity : 0.004 0.047 1763 Dihedral : 29.211 175.034 4680 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 14.90 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1019 helix: 2.35 (0.22), residues: 585 sheet: -2.87 (0.91), residues: 26 loop : -2.05 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS D 46 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR F 88 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.131 Fit side-chains REVERT: K 100 MET cc_start: 0.7213 (pmm) cc_final: 0.6809 (pmm) REVERT: K 218 TRP cc_start: 0.5196 (OUTLIER) cc_final: 0.4923 (p90) REVERT: K 253 MET cc_start: 0.8257 (mtp) cc_final: 0.7839 (mmp) REVERT: K 294 LEU cc_start: 0.6341 (tp) cc_final: 0.5080 (tp) REVERT: A 113 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7799 (m170) REVERT: D 97 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8974 (mp) REVERT: F 88 TYR cc_start: 0.8972 (m-10) cc_final: 0.8189 (m-80) REVERT: H 34 TYR cc_start: 0.8557 (m-80) cc_final: 0.8275 (m-80) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.2723 time to fit residues: 61.5314 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN F 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15749 Z= 0.232 Angle : 0.564 8.698 22623 Z= 0.327 Chirality : 0.034 0.152 2548 Planarity : 0.004 0.046 1763 Dihedral : 29.258 174.697 4680 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.96 % Allowed : 15.59 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1019 helix: 2.26 (0.22), residues: 587 sheet: -2.83 (0.89), residues: 26 loop : -2.08 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.004 0.001 HIS D 46 PHE 0.008 0.001 PHE A 104 TYR 0.021 0.001 TYR C 57 ARG 0.005 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.167 Fit side-chains REVERT: K 100 MET cc_start: 0.7226 (pmm) cc_final: 0.6774 (pmm) REVERT: K 218 TRP cc_start: 0.5123 (OUTLIER) cc_final: 0.4911 (p90) REVERT: K 253 MET cc_start: 0.8181 (mtp) cc_final: 0.7807 (mmp) REVERT: K 294 LEU cc_start: 0.6469 (tp) cc_final: 0.5376 (tp) REVERT: A 113 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7875 (m170) REVERT: D 97 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8957 (mp) REVERT: F 88 TYR cc_start: 0.9003 (m-10) cc_final: 0.8656 (m-80) outliers start: 17 outliers final: 11 residues processed: 153 average time/residue: 0.2674 time to fit residues: 59.5430 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15749 Z= 0.194 Angle : 0.544 8.969 22623 Z= 0.317 Chirality : 0.033 0.163 2548 Planarity : 0.003 0.044 1763 Dihedral : 29.142 174.989 4680 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.08 % Allowed : 15.94 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1019 helix: 2.43 (0.22), residues: 586 sheet: -2.73 (0.89), residues: 26 loop : -2.05 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS D 46 PHE 0.007 0.001 PHE K 281 TYR 0.017 0.001 TYR F 88 ARG 0.005 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.279 Fit side-chains REVERT: K 100 MET cc_start: 0.7101 (pmm) cc_final: 0.6127 (pmm) REVERT: K 218 TRP cc_start: 0.5192 (OUTLIER) cc_final: 0.4958 (p90) REVERT: K 253 MET cc_start: 0.8287 (mtp) cc_final: 0.7790 (mmp) REVERT: K 294 LEU cc_start: 0.6350 (tp) cc_final: 0.5190 (tp) REVERT: A 113 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7851 (m170) REVERT: F 88 TYR cc_start: 0.9006 (m-10) cc_final: 0.8710 (m-80) outliers start: 18 outliers final: 12 residues processed: 156 average time/residue: 0.2680 time to fit residues: 61.5223 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 0.0030 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 3.5998 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15749 Z= 0.250 Angle : 0.574 10.019 22623 Z= 0.333 Chirality : 0.034 0.152 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.233 174.606 4680 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.96 % Allowed : 16.17 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1019 helix: 2.25 (0.22), residues: 587 sheet: -2.67 (0.88), residues: 26 loop : -2.14 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.005 0.001 HIS D 46 PHE 0.008 0.001 PHE A 104 TYR 0.017 0.001 TYR F 88 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.185 Fit side-chains REVERT: K 100 MET cc_start: 0.7103 (pmm) cc_final: 0.6118 (pmm) REVERT: K 253 MET cc_start: 0.8152 (mtp) cc_final: 0.7826 (mmp) REVERT: K 294 LEU cc_start: 0.6459 (tp) cc_final: 0.5449 (tp) REVERT: K 307 TYR cc_start: 0.7345 (m-80) cc_final: 0.6517 (m-80) REVERT: A 113 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7864 (m170) REVERT: F 88 TYR cc_start: 0.8978 (m-10) cc_final: 0.8754 (m-80) REVERT: G 110 ASN cc_start: 0.8461 (p0) cc_final: 0.8244 (p0) outliers start: 17 outliers final: 14 residues processed: 148 average time/residue: 0.2838 time to fit residues: 60.5694 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.3980 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15749 Z= 0.264 Angle : 0.585 9.481 22623 Z= 0.338 Chirality : 0.035 0.155 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.292 174.536 4678 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.85 % Allowed : 16.63 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1019 helix: 2.24 (0.22), residues: 584 sheet: -2.60 (0.89), residues: 26 loop : -2.17 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 218 HIS 0.005 0.001 HIS D 46 PHE 0.008 0.001 PHE K 311 TYR 0.016 0.001 TYR F 88 ARG 0.007 0.000 ARG K 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.082 Fit side-chains REVERT: K 100 MET cc_start: 0.7093 (pmm) cc_final: 0.6068 (pmm) REVERT: K 253 MET cc_start: 0.8111 (mtp) cc_final: 0.7692 (mmp) REVERT: A 113 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7883 (m170) REVERT: F 88 TYR cc_start: 0.9004 (m-10) cc_final: 0.8783 (m-80) outliers start: 16 outliers final: 15 residues processed: 150 average time/residue: 0.2627 time to fit residues: 57.0129 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 64 optimal weight: 0.0570 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 1.5900 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15749 Z= 0.183 Angle : 0.549 10.513 22623 Z= 0.320 Chirality : 0.033 0.146 2548 Planarity : 0.004 0.053 1763 Dihedral : 29.142 175.275 4678 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.39 % Allowed : 17.55 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1019 helix: 2.47 (0.22), residues: 586 sheet: -2.54 (0.91), residues: 26 loop : -2.14 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE K 281 TYR 0.022 0.001 TYR F 88 ARG 0.003 0.000 ARG G 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.313 Fit side-chains REVERT: K 100 MET cc_start: 0.7129 (pmm) cc_final: 0.6064 (pmm) REVERT: A 113 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7854 (m170) outliers start: 12 outliers final: 11 residues processed: 149 average time/residue: 0.2724 time to fit residues: 59.1639 Evaluate side-chains 147 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.109886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073108 restraints weight = 38649.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074997 restraints weight = 20664.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076137 restraints weight = 14530.820| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15749 Z= 0.231 Angle : 0.580 11.646 22623 Z= 0.334 Chirality : 0.034 0.150 2548 Planarity : 0.004 0.053 1763 Dihedral : 29.211 174.676 4678 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.62 % Allowed : 17.32 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1019 helix: 2.32 (0.22), residues: 588 sheet: -2.54 (0.90), residues: 26 loop : -2.18 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 218 HIS 0.004 0.001 HIS F 18 PHE 0.007 0.001 PHE A 104 TYR 0.026 0.002 TYR F 88 ARG 0.004 0.000 ARG G 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.93 seconds wall clock time: 41 minutes 40.60 seconds (2500.60 seconds total)