Starting phenix.real_space_refine on Thu Feb 15 08:31:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go9_34174/02_2024/8go9_34174_updated.pdb" } resolution = 3.35 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= 0.039 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 12 5.49 5 S 26 5.16 5 C 7376 2.51 5 N 1988 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 400": "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: 11662 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2888 Classifications: {'peptide': 363} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2888 Classifications: {'peptide': 363} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335} Chain breaks: 1 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.54 Number of scatterers: 11662 At special positions: 0 Unit cell: (186.038, 87.6375, 121.463, 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 26 16.00 P 12 15.00 O 2260 8.00 N 1988 7.00 C 7376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 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: 4.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 28 sheets defined 5.5% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 46 through 49 No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 394 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.906A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP A 30 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 172 " --> pdb=" O ASP A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 165 through 169 removed outlier: 3.605A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 63 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 81 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 62 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP A 79 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 189 removed outlier: 3.530A pdb=" N THR A 187 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 271 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.845A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.668A pdb=" N VAL B 8 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 24 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.516A pdb=" N HIS B 38 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 161 through 163 Processing sheet with id= K, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= L, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.093A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 14 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU C 106 " --> pdb=" O ALA C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 86 through 91 removed outlier: 6.140A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= O, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.668A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 24 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.517A pdb=" N HIS D 38 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 161 through 163 Processing sheet with id= S, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= T, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.093A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA E 14 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU E 106 " --> pdb=" O ALA E 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 86 through 91 removed outlier: 6.139A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 117 through 119 Processing sheet with id= W, first strand: chain 'F' and resid 10 through 13 Processing sheet with id= X, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.906A pdb=" N ARG F 170 " --> pdb=" O PHE F 28 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP F 30 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL F 172 " --> pdb=" O ASP F 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 165 through 169 removed outlier: 3.605A pdb=" N ILE F 169 " --> pdb=" O PHE F 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 63 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE F 81 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 62 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP F 79 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 128 through 130 Processing sheet with id= AA, first strand: chain 'F' and resid 184 through 189 removed outlier: 3.529A pdb=" N THR F 187 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 271 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 336 through 342 removed outlier: 3.844A pdb=" N VAL F 336 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR F 322 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 232 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 255 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN F 238 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA F 240 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS F 251 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE F 242 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLN F 249 " --> pdb=" O ILE F 242 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3752 1.34 - 1.46: 2723 1.46 - 1.58: 5375 1.58 - 1.69: 46 1.69 - 1.81: 34 Bond restraints: 11930 Sorted by residual: bond pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O2P TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O2P TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 11925 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 420 106.90 - 113.67: 6666 113.67 - 120.44: 4050 120.44 - 127.21: 4986 127.21 - 133.98: 128 Bond angle restraints: 16250 Sorted by residual: angle pdb=" CB TPO H 354 " pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 119.31 107.22 12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB TPO G 354 " pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 119.31 107.27 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " pdb=" O1P TPO G 354 " ideal model delta sigma weight residual 100.43 109.46 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " pdb=" O1P TPO H 354 " ideal model delta sigma weight residual 100.43 109.43 -9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C LEU F 49 " pdb=" N LYS F 50 " pdb=" CA LYS F 50 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 ... (remaining 16245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6599 17.99 - 35.99: 463 35.99 - 53.98: 86 53.98 - 71.97: 16 71.97 - 89.96: 8 Dihedral angle restraints: 7172 sinusoidal: 2730 harmonic: 4442 Sorted by residual: dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta harmonic sigma weight residual 180.00 147.99 32.01 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA ARG F 96 " pdb=" C ARG F 96 " pdb=" N PRO F 97 " pdb=" CA PRO F 97 " ideal model delta harmonic sigma weight residual 180.00 148.06 31.94 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA PRO F 95 " pdb=" C PRO F 95 " pdb=" N ARG F 96 " pdb=" CA ARG F 96 " ideal model delta harmonic sigma weight residual 0.00 -30.10 30.10 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1290 0.035 - 0.071: 337 0.071 - 0.106: 157 0.106 - 0.141: 56 0.141 - 0.177: 4 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CA LYS A 295 " pdb=" N LYS A 295 " pdb=" C LYS A 295 " pdb=" CB LYS A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA LYS A 108 " pdb=" N LYS A 108 " pdb=" C LYS A 108 " pdb=" CB LYS A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LYS F 108 " pdb=" N LYS F 108 " pdb=" C LYS F 108 " pdb=" CB LYS F 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1841 not shown) Planarity restraints: 2078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 96 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO A 97 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 96 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO F 97 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO F 97 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 97 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 91 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 92 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.027 5.00e-02 4.00e+02 ... (remaining 2075 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2838 2.80 - 3.33: 9683 3.33 - 3.85: 17993 3.85 - 4.38: 20086 4.38 - 4.90: 36857 Nonbonded interactions: 87457 Sorted by model distance: nonbonded pdb=" OE1 GLN C 7 " pdb=" OG1 THR C 103 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLN E 7 " pdb=" OG1 THR E 103 " model vdw 2.277 2.440 nonbonded pdb=" NZ LYS F 11 " pdb=" OE2 GLU H 349 " model vdw 2.279 2.520 nonbonded pdb=" O PHE E 140 " pdb=" OG1 THR E 173 " model vdw 2.282 2.440 nonbonded pdb=" O PHE C 140 " pdb=" OG1 THR C 173 " model vdw 2.282 2.440 ... (remaining 87452 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'G' 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=0.65 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.640 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 31.630 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.108 11930 Z= 0.205 Angle : 0.554 12.092 16250 Z= 0.275 Chirality : 0.042 0.177 1844 Planarity : 0.006 0.114 2078 Dihedral : 13.071 89.963 4286 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.32 % Allowed : 0.24 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 2.13 % Twisted General : 0.14 % 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 (0.23), residues: 1472 helix: 2.08 (0.60), residues: 80 sheet: 1.27 (0.22), residues: 656 loop : -0.77 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 50 HIS 0.002 0.000 HIS F 346 PHE 0.008 0.001 PHE F 278 TYR 0.006 0.001 TYR A 250 ARG 0.007 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.351 Fit side-chains REVERT: A 108 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7923 (tttm) REVERT: B 77 THR cc_start: 0.8264 (p) cc_final: 0.8018 (p) REVERT: B 185 LEU cc_start: 0.7506 (mm) cc_final: 0.7219 (mm) REVERT: D 22 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7120 (tpt-90) REVERT: D 132 PHE cc_start: 0.6250 (m-10) cc_final: 0.5801 (m-80) REVERT: D 151 LEU cc_start: 0.7352 (tt) cc_final: 0.7145 (tt) REVERT: F 108 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7960 (ttpt) outliers start: 4 outliers final: 1 residues processed: 128 average time/residue: 0.2676 time to fit residues: 48.0709 Evaluate side-chains 107 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 295 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 87 ASN D 87 ASN ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11930 Z= 0.168 Angle : 0.500 6.990 16250 Z= 0.256 Chirality : 0.043 0.153 1844 Planarity : 0.005 0.091 2078 Dihedral : 5.627 63.538 1688 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.28 % Allowed : 5.66 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1472 helix: 2.31 (0.60), residues: 80 sheet: 1.06 (0.20), residues: 710 loop : -0.63 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.002 0.000 HIS F 199 PHE 0.020 0.001 PHE F 81 TYR 0.012 0.001 TYR A 250 ARG 0.005 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.398 Fit side-chains REVERT: A 308 LYS cc_start: 0.7505 (ptpp) cc_final: 0.6864 (mtpp) REVERT: B 185 LEU cc_start: 0.7531 (mm) cc_final: 0.6735 (mm) REVERT: D 185 LEU cc_start: 0.7498 (mm) cc_final: 0.6736 (mm) REVERT: F 153 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8441 (mttp) REVERT: F 230 LYS cc_start: 0.6859 (mtmm) cc_final: 0.6299 (ttpp) REVERT: F 308 LYS cc_start: 0.7647 (ptpp) cc_final: 0.6982 (mtpp) outliers start: 16 outliers final: 14 residues processed: 124 average time/residue: 0.2941 time to fit residues: 50.8165 Evaluate side-chains 113 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 296 HIS Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN C 38 GLN D 87 ASN E 38 GLN ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11930 Z= 0.212 Angle : 0.517 6.358 16250 Z= 0.261 Chirality : 0.043 0.152 1844 Planarity : 0.005 0.065 2078 Dihedral : 5.504 65.055 1680 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.52 % Allowed : 7.89 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.47 (0.23), residues: 1472 helix: 2.32 (0.60), residues: 80 sheet: 1.04 (0.20), residues: 692 loop : -0.68 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 50 HIS 0.002 0.001 HIS F 346 PHE 0.021 0.002 PHE F 269 TYR 0.014 0.001 TYR E 92 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.265 Fit side-chains REVERT: D 185 LEU cc_start: 0.7554 (mm) cc_final: 0.6744 (mm) REVERT: F 153 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8427 (mttp) REVERT: F 230 LYS cc_start: 0.6869 (mtmm) cc_final: 0.6492 (mtpp) REVERT: F 308 LYS cc_start: 0.7263 (ptpp) cc_final: 0.6993 (mtpp) outliers start: 19 outliers final: 19 residues processed: 130 average time/residue: 0.2793 time to fit residues: 50.1958 Evaluate side-chains 117 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS A 282 ASN B 87 ASN B 181 GLN D 87 ASN ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11930 Z= 0.249 Angle : 0.529 6.284 16250 Z= 0.269 Chirality : 0.044 0.156 1844 Planarity : 0.005 0.088 2078 Dihedral : 5.508 67.547 1676 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.67 % Allowed : 10.13 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1472 helix: 2.29 (0.60), residues: 82 sheet: 0.90 (0.20), residues: 692 loop : -0.73 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 50 HIS 0.003 0.001 HIS F 346 PHE 0.014 0.001 PHE F 81 TYR 0.018 0.002 TYR C 92 ARG 0.005 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.426 Fit side-chains REVERT: C 119 PHE cc_start: 0.4988 (m-80) cc_final: 0.4559 (m-80) REVERT: D 185 LEU cc_start: 0.7268 (mm) cc_final: 0.6478 (mm) REVERT: F 153 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8483 (mttp) REVERT: F 308 LYS cc_start: 0.7308 (ptpp) cc_final: 0.7031 (mtpp) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.2950 time to fit residues: 45.6642 Evaluate side-chains 106 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN B 87 ASN B 174 HIS D 87 ASN D 174 HIS ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11930 Z= 0.471 Angle : 0.655 9.765 16250 Z= 0.338 Chirality : 0.048 0.174 1844 Planarity : 0.005 0.073 2078 Dihedral : 6.140 74.268 1676 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.15 % Allowed : 11.08 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.19 (0.23), residues: 1472 helix: 1.98 (0.60), residues: 82 sheet: 0.55 (0.20), residues: 702 loop : -1.10 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 50 HIS 0.008 0.001 HIS A 211 PHE 0.024 0.002 PHE A 269 TYR 0.030 0.003 TYR E 92 ARG 0.005 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.334 Fit side-chains REVERT: A 63 ARG cc_start: 0.7256 (mtp85) cc_final: 0.7024 (mtp85) REVERT: B 68 LYS cc_start: 0.7859 (tptt) cc_final: 0.7637 (tptp) REVERT: C 109 ARG cc_start: 0.6923 (ptm160) cc_final: 0.6616 (ptm160) REVERT: D 68 LYS cc_start: 0.7841 (tptt) cc_final: 0.7633 (tptp) REVERT: F 153 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8547 (mttp) REVERT: F 230 LYS cc_start: 0.6965 (mtmm) cc_final: 0.6553 (mtpp) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.3041 time to fit residues: 51.9225 Evaluate side-chains 114 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11930 Z= 0.234 Angle : 0.551 7.114 16250 Z= 0.279 Chirality : 0.044 0.156 1844 Planarity : 0.005 0.062 2078 Dihedral : 5.800 72.068 1676 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.91 % Allowed : 12.12 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.05 (0.23), residues: 1472 helix: 2.29 (0.61), residues: 82 sheet: 0.70 (0.20), residues: 676 loop : -1.06 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.002 0.001 HIS D 38 PHE 0.025 0.002 PHE A 269 TYR 0.015 0.001 TYR E 92 ARG 0.011 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.584 Fit side-chains REVERT: B 68 LYS cc_start: 0.7793 (tptt) cc_final: 0.7572 (tptp) REVERT: D 68 LYS cc_start: 0.7784 (tptt) cc_final: 0.7570 (tptp) REVERT: E 28 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7499 (mm-40) REVERT: F 230 LYS cc_start: 0.7008 (mtmm) cc_final: 0.6591 (mtpp) outliers start: 24 outliers final: 24 residues processed: 105 average time/residue: 0.3782 time to fit residues: 54.4303 Evaluate side-chains 107 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN B 87 ASN D 87 ASN F 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11930 Z= 0.344 Angle : 0.593 8.025 16250 Z= 0.303 Chirality : 0.046 0.155 1844 Planarity : 0.005 0.059 2078 Dihedral : 5.976 73.837 1676 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.43 % Allowed : 10.61 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.28 (0.23), residues: 1472 helix: 2.21 (0.61), residues: 82 sheet: 0.40 (0.20), residues: 702 loop : -1.09 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 50 HIS 0.005 0.001 HIS F 211 PHE 0.027 0.002 PHE A 269 TYR 0.022 0.002 TYR C 92 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 1.348 Fit side-chains REVERT: A 74 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6635 (tp) REVERT: B 68 LYS cc_start: 0.7786 (tptt) cc_final: 0.7568 (tptp) REVERT: C 109 ARG cc_start: 0.6909 (ptm160) cc_final: 0.6562 (ptm160) REVERT: D 68 LYS cc_start: 0.7831 (tptt) cc_final: 0.7622 (tptp) REVERT: E 28 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7642 (mm-40) REVERT: E 110 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7622 (m) REVERT: F 74 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6644 (tp) REVERT: F 230 LYS cc_start: 0.7006 (mtmm) cc_final: 0.6602 (mtpp) outliers start: 43 outliers final: 35 residues processed: 125 average time/residue: 0.2554 time to fit residues: 44.6021 Evaluate side-chains 125 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 87 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN B 87 ASN C 28 GLN D 87 ASN F 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11930 Z= 0.185 Angle : 0.531 8.176 16250 Z= 0.268 Chirality : 0.044 0.155 1844 Planarity : 0.004 0.054 2078 Dihedral : 5.735 72.379 1676 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.55 % Allowed : 11.64 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1472 helix: 2.38 (0.61), residues: 82 sheet: 0.54 (0.20), residues: 700 loop : -0.99 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 50 HIS 0.002 0.000 HIS F 346 PHE 0.030 0.001 PHE A 269 TYR 0.012 0.001 TYR A 250 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 1.373 Fit side-chains REVERT: B 68 LYS cc_start: 0.7737 (tptt) cc_final: 0.7512 (tptp) REVERT: C 109 ARG cc_start: 0.6878 (ptm160) cc_final: 0.6537 (ptm160) REVERT: D 68 LYS cc_start: 0.7790 (tptt) cc_final: 0.7583 (tptp) REVERT: F 230 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6606 (mtpp) outliers start: 32 outliers final: 27 residues processed: 106 average time/residue: 0.2824 time to fit residues: 41.6976 Evaluate side-chains 110 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN B 87 ASN C 28 GLN C 161 GLN D 87 ASN E 28 GLN F 282 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 11930 Z= 0.403 Angle : 0.626 8.147 16250 Z= 0.322 Chirality : 0.047 0.160 1844 Planarity : 0.005 0.054 2078 Dihedral : 6.054 74.799 1676 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.95 % Allowed : 11.64 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.41 (0.23), residues: 1472 helix: 2.24 (0.61), residues: 82 sheet: 0.22 (0.20), residues: 722 loop : -1.12 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 50 HIS 0.007 0.001 HIS F 211 PHE 0.030 0.002 PHE A 269 TYR 0.025 0.002 TYR E 92 ARG 0.004 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 1.336 Fit side-chains REVERT: A 74 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6833 (mp) REVERT: B 68 LYS cc_start: 0.7825 (tptt) cc_final: 0.7611 (tptp) REVERT: D 68 LYS cc_start: 0.7814 (tptt) cc_final: 0.7612 (tptp) REVERT: F 230 LYS cc_start: 0.6977 (mtmm) cc_final: 0.6593 (mtpp) outliers start: 37 outliers final: 34 residues processed: 114 average time/residue: 0.2656 time to fit residues: 43.0827 Evaluate side-chains 123 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 28 GLN D 87 ASN E 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11930 Z= 0.354 Angle : 0.598 8.354 16250 Z= 0.307 Chirality : 0.046 0.156 1844 Planarity : 0.005 0.052 2078 Dihedral : 6.029 74.392 1676 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.03 % Allowed : 11.56 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.40 (0.23), residues: 1472 helix: 2.24 (0.61), residues: 82 sheet: 0.28 (0.20), residues: 702 loop : -1.14 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 50 HIS 0.006 0.001 HIS F 211 PHE 0.029 0.002 PHE A 269 TYR 0.022 0.002 TYR C 92 ARG 0.003 0.000 ARG D 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 87 time to evaluate : 1.331 Fit side-chains REVERT: B 68 LYS cc_start: 0.7807 (tptt) cc_final: 0.7599 (tptp) REVERT: F 230 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6630 (mtpp) outliers start: 38 outliers final: 35 residues processed: 114 average time/residue: 0.2742 time to fit residues: 44.0446 Evaluate side-chains 121 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 28 GLN D 87 ASN E 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136117 restraints weight = 14077.695| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.64 r_work: 0.3171 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11930 Z= 0.227 Angle : 0.550 8.681 16250 Z= 0.279 Chirality : 0.044 0.156 1844 Planarity : 0.004 0.052 2078 Dihedral : 5.854 73.055 1676 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.71 % Allowed : 11.88 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1472 helix: 2.35 (0.61), residues: 82 sheet: 0.41 (0.20), residues: 700 loop : -1.08 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.002 0.001 HIS D 38 PHE 0.026 0.002 PHE A 269 TYR 0.015 0.001 TYR C 92 ARG 0.004 0.000 ARG D 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.30 seconds wall clock time: 45 minutes 51.40 seconds (2751.40 seconds total)