Starting phenix.real_space_refine on Mon Nov 18 06:56:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/11_2024/8evj_28631.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 275 5.49 5 S 38 5.16 5 C 9198 2.51 5 N 2889 2.21 5 O 3551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15951 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2830 Classifications: {'DNA': 138} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 137} Chain: "I" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2825 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 748 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 10.04, per 1000 atoms: 0.63 Number of scatterers: 15951 At special positions: 0 Unit cell: (140.448, 121.44, 187.968, 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 38 16.00 P 275 15.00 O 3551 8.00 N 2889 7.00 C 9198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 22 sheets defined 46.7% alpha, 17.1% beta 132 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.771A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.459A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.803A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 93 removed outlier: 4.153A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.658A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.549A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.720A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.232A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.663A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.072A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.706A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.613A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.804A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.061A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.386A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.774A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.658A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 54 removed outlier: 3.971A pdb=" N TYR M 54 " --> pdb=" O PHE M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 4.104A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.993A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 4.221A pdb=" N GLN O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 220 Processing helix chain 'O' and resid 226 through 235 removed outlier: 3.637A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 241 removed outlier: 3.987A pdb=" N LYS O 239 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR O 240 " --> pdb=" O ASN O 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.670A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.823A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.589A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.517A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'M' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.957A pdb=" N GLU M 32 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.957A pdb=" N GLU M 32 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'M' and resid 168 through 171 removed outlier: 7.049A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 177 through 180 removed outlier: 4.013A pdb=" N VAL M 177 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 233 " --> pdb=" O VAL M 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB7, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.254A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR N 54 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR N 74 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.254A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC1, first strand: chain 'N' and resid 162 through 164 removed outlier: 4.083A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE N 233 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.447A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 206 through 207 Processing sheet with id=AC4, first strand: chain 'O' and resid 191 through 195 removed outlier: 6.162A pdb=" N TRP O 193 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN O 202 " --> pdb=" O TRP O 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP O 195 " --> pdb=" O THR O 200 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 324 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3957 1.34 - 1.46: 5327 1.46 - 1.58: 6924 1.58 - 1.70: 549 1.70 - 1.83: 61 Bond restraints: 16818 Sorted by residual: bond pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.24e+00 bond pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG GLN A 76 " pdb=" CD GLN A 76 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.27e+00 bond pdb=" C SER M 252 " pdb=" N PRO M 253 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.13e+00 ... (remaining 16813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23591 3.22 - 6.44: 249 6.44 - 9.66: 36 9.66 - 12.87: 8 12.87 - 16.09: 3 Bond angle restraints: 23887 Sorted by residual: angle pdb=" CA MET O 187 " pdb=" CB MET O 187 " pdb=" CG MET O 187 " ideal model delta sigma weight residual 114.10 125.32 -11.22 2.00e+00 2.50e-01 3.15e+01 angle pdb=" CB MET O 187 " pdb=" CG MET O 187 " pdb=" SD MET O 187 " ideal model delta sigma weight residual 112.70 128.79 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.40 118.15 -7.75 1.63e+00 3.76e-01 2.26e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 ... (remaining 23882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 7593 29.05 - 58.10: 1712 58.10 - 87.14: 151 87.14 - 116.19: 3 116.19 - 145.24: 1 Dihedral angle restraints: 9460 sinusoidal: 5682 harmonic: 3778 Sorted by residual: dihedral pdb=" C4' DT J 87 " pdb=" C3' DT J 87 " pdb=" O3' DT J 87 " pdb=" P DC J 88 " ideal model delta sinusoidal sigma weight residual 220.00 74.76 145.24 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA MET M 162 " pdb=" C MET M 162 " pdb=" N THR M 163 " pdb=" CA THR M 163 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 97 " pdb=" C LEU B 97 " pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2385 0.077 - 0.155: 264 0.155 - 0.232: 26 0.232 - 0.309: 4 0.309 - 0.387: 1 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB ILE M 56 " pdb=" CA ILE M 56 " pdb=" CG1 ILE M 56 " pdb=" CG2 ILE M 56 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR N 241 " pdb=" CA THR N 241 " pdb=" OG1 THR N 241 " pdb=" CG2 THR N 241 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2677 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.029 2.00e-02 2.50e+03 2.84e-02 1.62e+01 pdb=" CG TYR F 88 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO G 80 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 80 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.046 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3746 2.81 - 3.33: 14002 3.33 - 3.85: 31572 3.85 - 4.38: 34727 4.38 - 4.90: 51143 Nonbonded interactions: 135190 Sorted by model distance: nonbonded pdb=" OG1 THR N 128 " pdb=" OH TYR N 194 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU D 102 " pdb=" OH TYR N 54 " model vdw 2.287 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.300 3.040 nonbonded pdb=" O2 DC J 120 " pdb=" N2 DG I 43 " model vdw 2.305 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.305 3.040 ... (remaining 135185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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=1.00 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: 3.950 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.310 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.005 0.063 16818 Z= 0.280 Angle : 0.935 16.093 23887 Z= 0.510 Chirality : 0.050 0.387 2680 Planarity : 0.007 0.089 2052 Dihedral : 26.053 145.237 7023 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % 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: -1.52 (0.22), residues: 1275 helix: -0.97 (0.20), residues: 555 sheet: -0.02 (0.36), residues: 246 loop : -1.40 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 199 HIS 0.017 0.001 HIS B 75 PHE 0.020 0.002 PHE M 220 TYR 0.068 0.002 TYR F 88 ARG 0.015 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9407 (pttm) cc_final: 0.9194 (pttm) REVERT: A 106 ASP cc_start: 0.9099 (m-30) cc_final: 0.8793 (m-30) REVERT: C 74 LYS cc_start: 0.9574 (mptt) cc_final: 0.9299 (mmtt) REVERT: D 40 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9163 (pttm) REVERT: D 64 ASN cc_start: 0.9460 (m-40) cc_final: 0.9090 (m-40) REVERT: D 66 ILE cc_start: 0.9524 (mm) cc_final: 0.9247 (mm) REVERT: D 68 GLU cc_start: 0.8786 (mp0) cc_final: 0.8485 (mp0) REVERT: D 99 LEU cc_start: 0.9420 (mt) cc_final: 0.9187 (mp) REVERT: E 50 GLU cc_start: 0.9213 (pm20) cc_final: 0.8990 (pm20) REVERT: E 65 LEU cc_start: 0.9549 (tp) cc_final: 0.8959 (tp) REVERT: E 79 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8900 (ptmm) REVERT: E 105 GLU cc_start: 0.8905 (pp20) cc_final: 0.8495 (pp20) REVERT: E 106 ASP cc_start: 0.9347 (m-30) cc_final: 0.8730 (m-30) REVERT: F 49 LEU cc_start: 0.9637 (mt) cc_final: 0.9373 (mp) REVERT: F 59 LYS cc_start: 0.9449 (tmtt) cc_final: 0.8987 (tmtt) REVERT: F 84 MET cc_start: 0.8846 (tpt) cc_final: 0.8476 (tpp) REVERT: F 93 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8195 (tp30) REVERT: G 101 THR cc_start: 0.9455 (m) cc_final: 0.9186 (p) REVERT: H 65 ASP cc_start: 0.8914 (t0) cc_final: 0.8462 (t0) REVERT: H 68 GLU cc_start: 0.8777 (pp20) cc_final: 0.8565 (pp20) REVERT: H 73 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 76 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8380 (ttp-110) REVERT: M 235 ASN cc_start: 0.9510 (t0) cc_final: 0.9200 (t0) REVERT: N 42 MET cc_start: 0.9219 (pmm) cc_final: 0.8915 (pmm) REVERT: N 220 PHE cc_start: 0.9314 (m-80) cc_final: 0.8980 (m-80) REVERT: N 256 PHE cc_start: 0.8922 (m-80) cc_final: 0.8679 (m-80) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3199 time to fit residues: 122.6194 Evaluate side-chains 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0060 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN N 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16818 Z= 0.168 Angle : 0.582 7.330 23887 Z= 0.340 Chirality : 0.036 0.161 2680 Planarity : 0.005 0.069 2052 Dihedral : 29.316 143.583 4500 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -0.35 (0.23), residues: 1275 helix: 0.41 (0.21), residues: 571 sheet: 0.17 (0.36), residues: 240 loop : -1.16 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.030 0.001 TYR F 88 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9412 (pttm) cc_final: 0.9173 (pttm) REVERT: A 64 LYS cc_start: 0.9697 (mptt) cc_final: 0.9492 (mmtm) REVERT: A 106 ASP cc_start: 0.9178 (m-30) cc_final: 0.8962 (m-30) REVERT: B 49 LEU cc_start: 0.9305 (mp) cc_final: 0.8924 (tp) REVERT: D 54 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9220 (mtpt) REVERT: D 65 ASP cc_start: 0.9304 (t70) cc_final: 0.9058 (t0) REVERT: D 66 ILE cc_start: 0.9528 (mm) cc_final: 0.9232 (mm) REVERT: E 56 LYS cc_start: 0.9618 (ptpp) cc_final: 0.9393 (ptpp) REVERT: E 60 LEU cc_start: 0.9356 (mt) cc_final: 0.9036 (mt) REVERT: E 65 LEU cc_start: 0.9619 (tp) cc_final: 0.9041 (tp) REVERT: E 79 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8796 (tmmt) REVERT: E 89 VAL cc_start: 0.9605 (t) cc_final: 0.9162 (p) REVERT: E 90 MET cc_start: 0.9153 (mmp) cc_final: 0.8889 (mmm) REVERT: E 93 GLN cc_start: 0.8456 (tm-30) cc_final: 0.6891 (tm-30) REVERT: E 105 GLU cc_start: 0.8929 (pp20) cc_final: 0.8332 (pp20) REVERT: E 106 ASP cc_start: 0.9349 (m-30) cc_final: 0.8829 (m-30) REVERT: E 109 LEU cc_start: 0.9822 (mm) cc_final: 0.9540 (mm) REVERT: F 70 VAL cc_start: 0.9420 (p) cc_final: 0.8978 (p) REVERT: F 84 MET cc_start: 0.8789 (tpt) cc_final: 0.8183 (tpp) REVERT: F 93 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7995 (tm-30) REVERT: G 36 LYS cc_start: 0.9228 (mmtm) cc_final: 0.8834 (mmtm) REVERT: G 64 GLU cc_start: 0.8741 (tp30) cc_final: 0.8194 (tp30) REVERT: G 95 LYS cc_start: 0.9579 (tptt) cc_final: 0.9345 (ttmm) REVERT: H 56 MET cc_start: 0.9205 (tpp) cc_final: 0.8973 (tpp) REVERT: H 65 ASP cc_start: 0.8813 (t0) cc_final: 0.8255 (t0) REVERT: H 90 GLU cc_start: 0.9284 (mp0) cc_final: 0.9045 (mp0) REVERT: H 99 LEU cc_start: 0.9154 (mm) cc_final: 0.8930 (mm) REVERT: H 102 GLU cc_start: 0.8515 (pp20) cc_final: 0.8007 (pp20) REVERT: M 235 ASN cc_start: 0.9531 (t0) cc_final: 0.9195 (t0) REVERT: N 130 ASP cc_start: 0.9493 (p0) cc_final: 0.9211 (p0) REVERT: N 220 PHE cc_start: 0.9299 (m-80) cc_final: 0.9012 (m-80) REVERT: N 256 PHE cc_start: 0.8864 (m-80) cc_final: 0.8532 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3322 time to fit residues: 117.4943 Evaluate side-chains 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 73 ASN D 44 GLN M 65 GLN M 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16818 Z= 0.200 Angle : 0.590 9.604 23887 Z= 0.342 Chirality : 0.036 0.145 2680 Planarity : 0.004 0.062 2052 Dihedral : 29.212 145.336 4500 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.27 % Allowed : 4.33 % Favored : 95.40 % 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: 0.17 (0.23), residues: 1275 helix: 1.00 (0.21), residues: 576 sheet: 0.14 (0.35), residues: 252 loop : -1.00 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 193 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE H 62 TYR 0.029 0.001 TYR D 37 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 235 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9390 (pttm) cc_final: 0.9151 (pttm) REVERT: A 106 ASP cc_start: 0.9197 (m-30) cc_final: 0.8941 (m-30) REVERT: B 49 LEU cc_start: 0.9377 (mp) cc_final: 0.8773 (tp) REVERT: B 63 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8870 (pp20) REVERT: B 98 TYR cc_start: 0.9337 (m-80) cc_final: 0.8903 (m-80) REVERT: C 73 ASN cc_start: 0.9531 (OUTLIER) cc_final: 0.9179 (t0) REVERT: C 75 LYS cc_start: 0.9436 (mmmm) cc_final: 0.8989 (mmmm) REVERT: D 66 ILE cc_start: 0.9668 (mm) cc_final: 0.9404 (mm) REVERT: D 93 THR cc_start: 0.9516 (m) cc_final: 0.9111 (p) REVERT: E 65 LEU cc_start: 0.9648 (tp) cc_final: 0.9061 (tp) REVERT: E 81 ASP cc_start: 0.8893 (t70) cc_final: 0.8674 (t70) REVERT: E 93 GLN cc_start: 0.8945 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 97 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8577 (mt-10) REVERT: E 105 GLU cc_start: 0.8968 (pp20) cc_final: 0.8363 (pp20) REVERT: E 106 ASP cc_start: 0.9337 (m-30) cc_final: 0.8871 (m-30) REVERT: E 109 LEU cc_start: 0.9837 (mm) cc_final: 0.9499 (mm) REVERT: F 59 LYS cc_start: 0.9502 (tmtt) cc_final: 0.9062 (tmtt) REVERT: F 84 MET cc_start: 0.8938 (tpt) cc_final: 0.8317 (tpp) REVERT: F 93 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8142 (tm-30) REVERT: G 36 LYS cc_start: 0.9306 (mmtm) cc_final: 0.8933 (mmtm) REVERT: G 56 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8717 (mm-30) REVERT: G 61 GLU cc_start: 0.8952 (tp30) cc_final: 0.8645 (tt0) REVERT: G 64 GLU cc_start: 0.8740 (tp30) cc_final: 0.8201 (tp30) REVERT: G 95 LYS cc_start: 0.9616 (tptt) cc_final: 0.9398 (ttmm) REVERT: H 65 ASP cc_start: 0.9050 (t0) cc_final: 0.8628 (t0) REVERT: H 90 GLU cc_start: 0.9290 (mp0) cc_final: 0.9082 (mp0) REVERT: H 99 LEU cc_start: 0.9142 (mm) cc_final: 0.8893 (mm) REVERT: H 102 GLU cc_start: 0.8214 (pp20) cc_final: 0.7871 (pp20) REVERT: M 235 ASN cc_start: 0.9561 (t0) cc_final: 0.9196 (t0) REVERT: M 262 LEU cc_start: 0.9250 (tp) cc_final: 0.8992 (tt) REVERT: N 220 PHE cc_start: 0.9331 (m-80) cc_final: 0.9124 (m-80) REVERT: N 256 PHE cc_start: 0.8834 (m-80) cc_final: 0.8513 (m-80) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.3304 time to fit residues: 110.9294 Evaluate side-chains 187 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 40.0000 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16818 Z= 0.168 Angle : 0.576 9.118 23887 Z= 0.334 Chirality : 0.036 0.149 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.038 144.519 4500 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % 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: 0.46 (0.24), residues: 1275 helix: 1.25 (0.22), residues: 574 sheet: 0.34 (0.36), residues: 250 loop : -0.88 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 193 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE H 62 TYR 0.024 0.001 TYR D 37 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9193 (m-30) cc_final: 0.8929 (m-30) REVERT: B 49 LEU cc_start: 0.9406 (mp) cc_final: 0.8476 (tp) REVERT: B 53 GLU cc_start: 0.9007 (mp0) cc_final: 0.8670 (pm20) REVERT: B 98 TYR cc_start: 0.9386 (m-80) cc_final: 0.8958 (m-80) REVERT: C 73 ASN cc_start: 0.9486 (t0) cc_final: 0.9171 (t0) REVERT: C 75 LYS cc_start: 0.9441 (mmmm) cc_final: 0.8977 (mmmm) REVERT: D 66 ILE cc_start: 0.9677 (mm) cc_final: 0.9396 (mm) REVERT: D 83 ARG cc_start: 0.8774 (mmp80) cc_final: 0.8477 (mmp80) REVERT: E 50 GLU cc_start: 0.9184 (pm20) cc_final: 0.8954 (pm20) REVERT: E 60 LEU cc_start: 0.9540 (mt) cc_final: 0.9336 (mp) REVERT: E 65 LEU cc_start: 0.9679 (tp) cc_final: 0.9096 (tp) REVERT: E 93 GLN cc_start: 0.8811 (tm-30) cc_final: 0.7086 (tm-30) REVERT: E 97 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 105 GLU cc_start: 0.8957 (pp20) cc_final: 0.8514 (pp20) REVERT: E 106 ASP cc_start: 0.9319 (m-30) cc_final: 0.8890 (m-30) REVERT: E 109 LEU cc_start: 0.9828 (mm) cc_final: 0.9513 (mm) REVERT: F 59 LYS cc_start: 0.9696 (tmtt) cc_final: 0.8660 (tmtt) REVERT: F 63 GLU cc_start: 0.9159 (pt0) cc_final: 0.8645 (pt0) REVERT: F 84 MET cc_start: 0.8812 (tpt) cc_final: 0.8095 (tpp) REVERT: F 93 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8161 (tm-30) REVERT: G 36 LYS cc_start: 0.9363 (mmtm) cc_final: 0.9013 (mmtm) REVERT: G 64 GLU cc_start: 0.8809 (tp30) cc_final: 0.8347 (tp30) REVERT: G 95 LYS cc_start: 0.9596 (tptt) cc_final: 0.9378 (ttmm) REVERT: H 65 ASP cc_start: 0.9036 (t0) cc_final: 0.8625 (t0) REVERT: H 73 GLU cc_start: 0.9418 (tp30) cc_final: 0.9096 (tp30) REVERT: H 76 ARG cc_start: 0.9492 (ttm-80) cc_final: 0.9168 (ttm110) REVERT: H 90 GLU cc_start: 0.9266 (mp0) cc_final: 0.9040 (mp0) REVERT: H 99 LEU cc_start: 0.9131 (mm) cc_final: 0.8861 (mm) REVERT: H 102 GLU cc_start: 0.8332 (pp20) cc_final: 0.8038 (pp20) REVERT: M 162 MET cc_start: 0.8102 (ppp) cc_final: 0.7746 (ppp) REVERT: M 235 ASN cc_start: 0.9546 (t0) cc_final: 0.9142 (t0) REVERT: M 262 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tt) REVERT: N 130 ASP cc_start: 0.9519 (p0) cc_final: 0.9267 (p0) REVERT: N 256 PHE cc_start: 0.8801 (m-80) cc_final: 0.8476 (m-80) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.3480 time to fit residues: 119.7902 Evaluate side-chains 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0870 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 70.0000 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 HIS ** N 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16818 Z= 0.167 Angle : 0.584 9.619 23887 Z= 0.336 Chirality : 0.036 0.198 2680 Planarity : 0.004 0.059 2052 Dihedral : 28.940 144.546 4500 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.60 (0.24), residues: 1275 helix: 1.36 (0.22), residues: 574 sheet: 0.43 (0.36), residues: 250 loop : -0.82 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 215 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.035 0.001 TYR H 80 ARG 0.003 0.000 ARG M 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9386 (pttm) cc_final: 0.9162 (pttm) REVERT: A 106 ASP cc_start: 0.9155 (m-30) cc_final: 0.8892 (m-30) REVERT: B 49 LEU cc_start: 0.9444 (mp) cc_final: 0.8839 (tp) REVERT: B 63 GLU cc_start: 0.9278 (pm20) cc_final: 0.8998 (pm20) REVERT: B 98 TYR cc_start: 0.9381 (m-10) cc_final: 0.8979 (m-80) REVERT: C 51 MET cc_start: 0.9385 (mmm) cc_final: 0.8954 (mmm) REVERT: C 55 LEU cc_start: 0.9729 (mt) cc_final: 0.9450 (mt) REVERT: C 73 ASN cc_start: 0.9490 (t0) cc_final: 0.9155 (t0) REVERT: C 75 LYS cc_start: 0.9443 (mmmm) cc_final: 0.9031 (mmmm) REVERT: D 66 ILE cc_start: 0.9645 (mm) cc_final: 0.9352 (mm) REVERT: E 50 GLU cc_start: 0.9208 (pm20) cc_final: 0.8969 (pm20) REVERT: E 60 LEU cc_start: 0.9531 (mt) cc_final: 0.8960 (mp) REVERT: E 65 LEU cc_start: 0.9675 (tp) cc_final: 0.9057 (tp) REVERT: E 93 GLN cc_start: 0.8743 (tm-30) cc_final: 0.6850 (tm-30) REVERT: E 97 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8220 (mt-10) REVERT: E 105 GLU cc_start: 0.8956 (pp20) cc_final: 0.8488 (pp20) REVERT: E 106 ASP cc_start: 0.9311 (m-30) cc_final: 0.8882 (m-30) REVERT: E 109 LEU cc_start: 0.9832 (mm) cc_final: 0.9502 (mm) REVERT: F 59 LYS cc_start: 0.9682 (tmtt) cc_final: 0.9317 (tmtt) REVERT: F 84 MET cc_start: 0.8795 (tpt) cc_final: 0.8026 (tpp) REVERT: F 93 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8190 (tm-30) REVERT: G 36 LYS cc_start: 0.9383 (mmtm) cc_final: 0.9118 (mmtm) REVERT: G 61 GLU cc_start: 0.8803 (tp30) cc_final: 0.8442 (tp30) REVERT: G 64 GLU cc_start: 0.8703 (tp30) cc_final: 0.8232 (tp30) REVERT: G 95 LYS cc_start: 0.9607 (tptt) cc_final: 0.9379 (ttmm) REVERT: H 65 ASP cc_start: 0.8963 (t0) cc_final: 0.8590 (t0) REVERT: H 90 GLU cc_start: 0.9260 (mp0) cc_final: 0.8993 (mp0) REVERT: H 99 LEU cc_start: 0.9146 (mm) cc_final: 0.8841 (mm) REVERT: M 235 ASN cc_start: 0.9528 (t0) cc_final: 0.9105 (t0) REVERT: M 262 LEU cc_start: 0.9248 (tp) cc_final: 0.8995 (tt) REVERT: N 103 MET cc_start: 0.9174 (tpt) cc_final: 0.8852 (tpt) REVERT: N 130 ASP cc_start: 0.9508 (p0) cc_final: 0.9233 (p0) REVERT: N 193 TRP cc_start: 0.8854 (m100) cc_final: 0.8425 (m100) REVERT: N 256 PHE cc_start: 0.8791 (m-80) cc_final: 0.8465 (m-80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3366 time to fit residues: 115.0734 Evaluate side-chains 199 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 145 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN N 195 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16818 Z= 0.295 Angle : 0.634 11.930 23887 Z= 0.363 Chirality : 0.038 0.152 2680 Planarity : 0.004 0.061 2052 Dihedral : 29.299 146.603 4500 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 0.63 (0.24), residues: 1275 helix: 1.37 (0.22), residues: 574 sheet: 0.18 (0.36), residues: 256 loop : -0.61 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 215 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.002 PHE N 220 TYR 0.028 0.002 TYR C 57 ARG 0.006 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9200 (m-30) cc_final: 0.8925 (m-30) REVERT: B 53 GLU cc_start: 0.9127 (mp0) cc_final: 0.8864 (pm20) REVERT: B 98 TYR cc_start: 0.9344 (m-10) cc_final: 0.9086 (m-80) REVERT: C 36 LYS cc_start: 0.9277 (mptt) cc_final: 0.9047 (mmtm) REVERT: C 51 MET cc_start: 0.9399 (mmm) cc_final: 0.9161 (mmm) REVERT: C 64 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8862 (mm-30) REVERT: C 73 ASN cc_start: 0.9622 (t0) cc_final: 0.9312 (t0) REVERT: C 75 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9184 (mmmm) REVERT: C 104 GLN cc_start: 0.8780 (mp10) cc_final: 0.8558 (mp10) REVERT: D 66 ILE cc_start: 0.9746 (mm) cc_final: 0.9510 (mm) REVERT: D 99 LEU cc_start: 0.9398 (mt) cc_final: 0.9144 (mp) REVERT: E 60 LEU cc_start: 0.9624 (mt) cc_final: 0.9320 (mt) REVERT: E 64 LYS cc_start: 0.9698 (mppt) cc_final: 0.9429 (mmtm) REVERT: E 90 MET cc_start: 0.9282 (mmp) cc_final: 0.9055 (mmp) REVERT: E 93 GLN cc_start: 0.8828 (tm-30) cc_final: 0.7047 (tm-30) REVERT: E 105 GLU cc_start: 0.9003 (pp20) cc_final: 0.8617 (pp20) REVERT: E 106 ASP cc_start: 0.9291 (m-30) cc_final: 0.8814 (m-30) REVERT: E 109 LEU cc_start: 0.9806 (mm) cc_final: 0.9464 (mm) REVERT: F 59 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9239 (tmtt) REVERT: F 84 MET cc_start: 0.8925 (tpt) cc_final: 0.8330 (tpp) REVERT: F 93 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8389 (tm-30) REVERT: G 61 GLU cc_start: 0.8985 (tp30) cc_final: 0.8619 (tp30) REVERT: G 64 GLU cc_start: 0.8763 (tp30) cc_final: 0.8202 (tp30) REVERT: G 89 ASN cc_start: 0.9529 (m-40) cc_final: 0.9243 (m-40) REVERT: G 95 LYS cc_start: 0.9679 (tptt) cc_final: 0.9468 (ttmm) REVERT: H 40 LYS cc_start: 0.9730 (ttpt) cc_final: 0.9463 (ttpp) REVERT: H 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8624 (t0) REVERT: H 73 GLU cc_start: 0.9379 (tp30) cc_final: 0.8738 (tp30) REVERT: H 76 ARG cc_start: 0.9505 (ttm-80) cc_final: 0.9061 (ttm110) REVERT: H 90 GLU cc_start: 0.9252 (mp0) cc_final: 0.9026 (mp0) REVERT: M 42 MET cc_start: 0.9262 (pmm) cc_final: 0.9048 (pmm) REVERT: M 262 LEU cc_start: 0.9313 (tp) cc_final: 0.9026 (tt) REVERT: N 103 MET cc_start: 0.9172 (tpt) cc_final: 0.8855 (tpt) REVERT: N 193 TRP cc_start: 0.8821 (m100) cc_final: 0.8471 (m100) REVERT: N 256 PHE cc_start: 0.8865 (m-80) cc_final: 0.8484 (m-80) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3219 time to fit residues: 103.0301 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16818 Z= 0.200 Angle : 0.609 10.835 23887 Z= 0.346 Chirality : 0.037 0.167 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.170 144.430 4500 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 (0.24), residues: 1275 helix: 1.47 (0.22), residues: 574 sheet: 0.18 (0.36), residues: 256 loop : -0.55 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 215 HIS 0.011 0.001 HIS F 75 PHE 0.012 0.001 PHE A 67 TYR 0.031 0.001 TYR H 80 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8891 (tp40) REVERT: A 97 GLU cc_start: 0.9004 (mp0) cc_final: 0.8584 (mp0) REVERT: A 106 ASP cc_start: 0.9153 (m-30) cc_final: 0.8914 (m-30) REVERT: B 58 LEU cc_start: 0.9773 (tt) cc_final: 0.9554 (tt) REVERT: B 62 LEU cc_start: 0.9791 (mp) cc_final: 0.9556 (mp) REVERT: B 98 TYR cc_start: 0.9377 (m-10) cc_final: 0.9083 (m-80) REVERT: C 51 MET cc_start: 0.9414 (mmm) cc_final: 0.8992 (mmm) REVERT: C 55 LEU cc_start: 0.9792 (mt) cc_final: 0.9485 (mt) REVERT: C 73 ASN cc_start: 0.9599 (t0) cc_final: 0.9277 (t0) REVERT: C 75 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9185 (mmmm) REVERT: C 104 GLN cc_start: 0.8741 (mp10) cc_final: 0.8451 (mp10) REVERT: D 66 ILE cc_start: 0.9717 (mm) cc_final: 0.9456 (mm) REVERT: D 99 LEU cc_start: 0.9354 (mt) cc_final: 0.9093 (mp) REVERT: E 64 LYS cc_start: 0.9670 (mppt) cc_final: 0.9449 (mmtm) REVERT: E 65 LEU cc_start: 0.9660 (tp) cc_final: 0.9076 (tp) REVERT: E 68 GLN cc_start: 0.8984 (pp30) cc_final: 0.8751 (pp30) REVERT: E 90 MET cc_start: 0.9261 (mmp) cc_final: 0.9048 (mmp) REVERT: E 93 GLN cc_start: 0.9015 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 97 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8741 (mm-30) REVERT: E 105 GLU cc_start: 0.8963 (pp20) cc_final: 0.8558 (pp20) REVERT: E 106 ASP cc_start: 0.9299 (m-30) cc_final: 0.8929 (m-30) REVERT: E 109 LEU cc_start: 0.9819 (mm) cc_final: 0.9480 (mm) REVERT: F 59 LYS cc_start: 0.9681 (tmtt) cc_final: 0.9283 (tmtt) REVERT: F 84 MET cc_start: 0.8699 (tpt) cc_final: 0.7853 (tpp) REVERT: F 93 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8308 (tm-30) REVERT: G 57 TYR cc_start: 0.9107 (t80) cc_final: 0.8869 (t80) REVERT: G 61 GLU cc_start: 0.8933 (tp30) cc_final: 0.8527 (tp30) REVERT: G 64 GLU cc_start: 0.8714 (tp30) cc_final: 0.8110 (tp30) REVERT: G 95 LYS cc_start: 0.9644 (tptt) cc_final: 0.9425 (ttmm) REVERT: H 40 LYS cc_start: 0.9745 (ttpt) cc_final: 0.9484 (ttpp) REVERT: H 65 ASP cc_start: 0.9120 (t0) cc_final: 0.8724 (t0) REVERT: H 90 GLU cc_start: 0.9297 (mp0) cc_final: 0.9051 (mp0) REVERT: M 76 TYR cc_start: 0.8889 (t80) cc_final: 0.8657 (t80) REVERT: M 162 MET cc_start: 0.8168 (ppp) cc_final: 0.7824 (ppp) REVERT: M 262 LEU cc_start: 0.9312 (tp) cc_final: 0.9038 (tt) REVERT: N 103 MET cc_start: 0.9182 (tpt) cc_final: 0.8879 (tpt) REVERT: N 256 PHE cc_start: 0.8804 (m-80) cc_final: 0.8436 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3356 time to fit residues: 110.3246 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16818 Z= 0.285 Angle : 0.648 11.282 23887 Z= 0.368 Chirality : 0.038 0.160 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.306 146.244 4500 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.63 (0.24), residues: 1275 helix: 1.40 (0.21), residues: 575 sheet: 0.08 (0.36), residues: 256 loop : -0.57 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 193 HIS 0.008 0.001 HIS F 75 PHE 0.014 0.002 PHE G 25 TYR 0.023 0.002 TYR F 51 ARG 0.005 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9393 (pttm) cc_final: 0.9183 (pttm) REVERT: A 79 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8973 (mtmt) REVERT: A 106 ASP cc_start: 0.9217 (m-30) cc_final: 0.8982 (m-30) REVERT: B 98 TYR cc_start: 0.9360 (m-10) cc_final: 0.9152 (m-80) REVERT: C 51 MET cc_start: 0.9406 (mmm) cc_final: 0.9193 (mmm) REVERT: C 64 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8936 (mm-30) REVERT: C 73 ASN cc_start: 0.9652 (t0) cc_final: 0.9352 (t0) REVERT: C 75 LYS cc_start: 0.9455 (mmmm) cc_final: 0.9210 (mmmm) REVERT: D 54 LYS cc_start: 0.9741 (mmmm) cc_final: 0.9540 (mmmm) REVERT: D 66 ILE cc_start: 0.9741 (mm) cc_final: 0.9495 (mm) REVERT: D 68 GLU cc_start: 0.8664 (mp0) cc_final: 0.8380 (mp0) REVERT: D 99 LEU cc_start: 0.9313 (mt) cc_final: 0.9030 (mp) REVERT: E 60 LEU cc_start: 0.9482 (mt) cc_final: 0.9263 (mp) REVERT: E 64 LYS cc_start: 0.9693 (mppt) cc_final: 0.9403 (mmtm) REVERT: E 68 GLN cc_start: 0.9060 (pp30) cc_final: 0.8854 (pp30) REVERT: E 90 MET cc_start: 0.9289 (mmp) cc_final: 0.9084 (mmp) REVERT: E 93 GLN cc_start: 0.9067 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 105 GLU cc_start: 0.8954 (pp20) cc_final: 0.8548 (pp20) REVERT: E 106 ASP cc_start: 0.9338 (m-30) cc_final: 0.8937 (m-30) REVERT: E 109 LEU cc_start: 0.9820 (mm) cc_final: 0.9457 (mm) REVERT: F 84 MET cc_start: 0.8982 (tpt) cc_final: 0.8741 (tpp) REVERT: F 88 TYR cc_start: 0.8999 (m-10) cc_final: 0.8329 (m-10) REVERT: F 93 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8445 (tm-30) REVERT: G 56 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8878 (mm-30) REVERT: G 57 TYR cc_start: 0.9071 (t80) cc_final: 0.8776 (t80) REVERT: G 61 GLU cc_start: 0.8972 (tp30) cc_final: 0.8524 (tp30) REVERT: G 64 GLU cc_start: 0.8719 (tp30) cc_final: 0.8171 (tp30) REVERT: G 82 HIS cc_start: 0.9241 (m90) cc_final: 0.8988 (m90) REVERT: G 95 LYS cc_start: 0.9678 (tptt) cc_final: 0.9474 (ttmm) REVERT: H 40 LYS cc_start: 0.9735 (ttpt) cc_final: 0.9480 (ttpp) REVERT: H 65 ASP cc_start: 0.9108 (t0) cc_final: 0.8650 (t0) REVERT: H 76 ARG cc_start: 0.9480 (ttm-80) cc_final: 0.9123 (ttm110) REVERT: H 90 GLU cc_start: 0.9170 (mp0) cc_final: 0.8828 (mp0) REVERT: M 42 MET cc_start: 0.9290 (pmm) cc_final: 0.9066 (pmm) REVERT: M 162 MET cc_start: 0.8232 (ppp) cc_final: 0.7728 (ppp) REVERT: M 262 LEU cc_start: 0.9327 (tp) cc_final: 0.9053 (tt) REVERT: N 103 MET cc_start: 0.9141 (tpt) cc_final: 0.8910 (tpt) REVERT: N 220 PHE cc_start: 0.9269 (m-80) cc_final: 0.9055 (m-80) REVERT: N 256 PHE cc_start: 0.8932 (m-80) cc_final: 0.8515 (m-80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3368 time to fit residues: 105.4352 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16818 Z= 0.252 Angle : 0.650 11.497 23887 Z= 0.368 Chirality : 0.038 0.187 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.317 144.939 4500 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.60 (0.24), residues: 1275 helix: 1.32 (0.21), residues: 578 sheet: 0.22 (0.36), residues: 250 loop : -0.61 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP N 193 HIS 0.012 0.001 HIS F 75 PHE 0.021 0.001 PHE A 67 TYR 0.023 0.001 TYR F 51 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9391 (pttm) cc_final: 0.9185 (pttm) REVERT: A 106 ASP cc_start: 0.9191 (m-30) cc_final: 0.8973 (m-30) REVERT: A 120 MET cc_start: 0.8546 (ptp) cc_final: 0.8145 (mpp) REVERT: B 98 TYR cc_start: 0.9359 (m-10) cc_final: 0.9089 (m-80) REVERT: C 51 MET cc_start: 0.9416 (mmm) cc_final: 0.9012 (mmm) REVERT: C 55 LEU cc_start: 0.9812 (mt) cc_final: 0.9502 (mt) REVERT: C 73 ASN cc_start: 0.9671 (t0) cc_final: 0.9299 (t0) REVERT: C 104 GLN cc_start: 0.8819 (mp10) cc_final: 0.8610 (mp10) REVERT: D 65 ASP cc_start: 0.9330 (t70) cc_final: 0.9072 (t0) REVERT: D 66 ILE cc_start: 0.9716 (mm) cc_final: 0.9450 (mm) REVERT: D 68 GLU cc_start: 0.8596 (mp0) cc_final: 0.8243 (mp0) REVERT: E 60 LEU cc_start: 0.9583 (mt) cc_final: 0.8643 (mp) REVERT: E 64 LYS cc_start: 0.9692 (mppt) cc_final: 0.9442 (mmtm) REVERT: E 65 LEU cc_start: 0.9680 (tp) cc_final: 0.9143 (tp) REVERT: E 93 GLN cc_start: 0.8812 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 97 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8010 (mt-10) REVERT: E 105 GLU cc_start: 0.9011 (pp20) cc_final: 0.8612 (pp20) REVERT: E 106 ASP cc_start: 0.9304 (m-30) cc_final: 0.8904 (m-30) REVERT: E 109 LEU cc_start: 0.9825 (mm) cc_final: 0.9445 (mm) REVERT: F 59 LYS cc_start: 0.9532 (tmtt) cc_final: 0.8891 (tmtt) REVERT: F 84 MET cc_start: 0.8931 (tpt) cc_final: 0.8580 (tpp) REVERT: F 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8228 (m-10) REVERT: F 93 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 57 TYR cc_start: 0.9066 (t80) cc_final: 0.8794 (t80) REVERT: G 61 GLU cc_start: 0.8937 (tp30) cc_final: 0.8518 (tp30) REVERT: G 64 GLU cc_start: 0.8688 (tp30) cc_final: 0.8131 (tp30) REVERT: H 40 LYS cc_start: 0.9736 (ttpt) cc_final: 0.9462 (ttpp) REVERT: H 65 ASP cc_start: 0.9071 (t0) cc_final: 0.8483 (t0) REVERT: H 76 ARG cc_start: 0.9467 (ttm-80) cc_final: 0.9232 (ttp-110) REVERT: H 90 GLU cc_start: 0.9149 (mp0) cc_final: 0.8857 (mp0) REVERT: M 262 LEU cc_start: 0.9338 (tp) cc_final: 0.9067 (tt) REVERT: N 220 PHE cc_start: 0.9278 (m-80) cc_final: 0.9042 (m-80) REVERT: N 256 PHE cc_start: 0.8876 (m-80) cc_final: 0.8455 (m-80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3296 time to fit residues: 102.7628 Evaluate side-chains 183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16818 Z= 0.235 Angle : 0.643 11.015 23887 Z= 0.363 Chirality : 0.038 0.176 2680 Planarity : 0.004 0.058 2052 Dihedral : 29.269 144.638 4500 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.61 (0.24), residues: 1275 helix: 1.37 (0.21), residues: 575 sheet: 0.07 (0.36), residues: 256 loop : -0.56 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 193 HIS 0.011 0.002 HIS F 75 PHE 0.015 0.001 PHE A 67 TYR 0.018 0.001 TYR D 37 ARG 0.005 0.000 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9389 (pttm) cc_final: 0.9176 (pttm) REVERT: A 106 ASP cc_start: 0.9164 (m-30) cc_final: 0.8917 (m-30) REVERT: A 120 MET cc_start: 0.8510 (ptp) cc_final: 0.8077 (mpp) REVERT: B 98 TYR cc_start: 0.9340 (m-10) cc_final: 0.9062 (m-80) REVERT: C 51 MET cc_start: 0.9391 (mmm) cc_final: 0.8973 (mmm) REVERT: C 55 LEU cc_start: 0.9804 (mt) cc_final: 0.9475 (mt) REVERT: C 73 ASN cc_start: 0.9661 (t0) cc_final: 0.9298 (t0) REVERT: C 104 GLN cc_start: 0.8794 (mp10) cc_final: 0.8531 (mp10) REVERT: D 65 ASP cc_start: 0.9309 (t70) cc_final: 0.9075 (t0) REVERT: D 66 ILE cc_start: 0.9715 (mm) cc_final: 0.9446 (mm) REVERT: D 68 GLU cc_start: 0.8573 (mp0) cc_final: 0.8184 (mp0) REVERT: D 83 ARG cc_start: 0.8662 (mmp80) cc_final: 0.8390 (mmp80) REVERT: D 99 LEU cc_start: 0.9413 (mt) cc_final: 0.9190 (mp) REVERT: E 60 LEU cc_start: 0.9553 (mt) cc_final: 0.9001 (mt) REVERT: E 64 LYS cc_start: 0.9673 (mppt) cc_final: 0.9437 (mmtm) REVERT: E 65 LEU cc_start: 0.9670 (tp) cc_final: 0.9147 (tp) REVERT: E 93 GLN cc_start: 0.8867 (tm-30) cc_final: 0.6793 (tm-30) REVERT: E 97 GLU cc_start: 0.8766 (mm-30) cc_final: 0.7789 (mm-30) REVERT: E 105 GLU cc_start: 0.8987 (pp20) cc_final: 0.8573 (pp20) REVERT: E 106 ASP cc_start: 0.9276 (m-30) cc_final: 0.8829 (m-30) REVERT: E 109 LEU cc_start: 0.9819 (mm) cc_final: 0.9422 (mm) REVERT: F 59 LYS cc_start: 0.9627 (tmtt) cc_final: 0.8485 (tmtt) REVERT: F 63 GLU cc_start: 0.9184 (pt0) cc_final: 0.8446 (pt0) REVERT: F 84 MET cc_start: 0.8868 (tpt) cc_final: 0.8477 (tpp) REVERT: F 88 TYR cc_start: 0.8916 (m-10) cc_final: 0.8118 (m-10) REVERT: F 93 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8337 (tm-30) REVERT: G 56 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8966 (mm-30) REVERT: G 64 GLU cc_start: 0.8729 (tp30) cc_final: 0.8207 (tp30) REVERT: H 40 LYS cc_start: 0.9726 (ttpt) cc_final: 0.9459 (ttpp) REVERT: H 65 ASP cc_start: 0.9059 (t0) cc_final: 0.8443 (t0) REVERT: H 90 GLU cc_start: 0.9155 (mp0) cc_final: 0.8846 (mp0) REVERT: M 42 MET cc_start: 0.9307 (pmm) cc_final: 0.9097 (pmm) REVERT: M 162 MET cc_start: 0.8339 (ppp) cc_final: 0.7960 (ppp) REVERT: M 262 LEU cc_start: 0.9338 (tp) cc_final: 0.9079 (tt) REVERT: N 42 MET cc_start: 0.9452 (pmm) cc_final: 0.9162 (pmm) REVERT: N 220 PHE cc_start: 0.9268 (m-80) cc_final: 0.9037 (m-80) REVERT: N 256 PHE cc_start: 0.8850 (m-80) cc_final: 0.8417 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3275 time to fit residues: 105.0393 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 122 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 104 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.032799 restraints weight = 117350.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033235 restraints weight = 58969.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.033724 restraints weight = 37229.515| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16818 Z= 0.363 Angle : 0.720 12.544 23887 Z= 0.403 Chirality : 0.040 0.243 2680 Planarity : 0.005 0.058 2052 Dihedral : 29.607 146.508 4500 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.44 (0.24), residues: 1275 helix: 1.25 (0.21), residues: 575 sheet: -0.03 (0.35), residues: 250 loop : -0.68 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 193 HIS 0.012 0.002 HIS G 82 PHE 0.018 0.002 PHE N 220 TYR 0.026 0.002 TYR M 76 ARG 0.007 0.001 ARG H 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.88 seconds wall clock time: 55 minutes 57.57 seconds (3357.57 seconds total)