Starting phenix.real_space_refine on Mon Mar 11 13:35:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjf_31620/03_2024/7fjf_31620.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5352 2.51 5 N 1370 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 52": "NH1" <-> "NH2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "f PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 185": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "m ARG 269": "NH1" <-> "NH2" Residue "n ARG 228": "NH1" <-> "NH2" Residue "n ARG 246": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8377 Number of models: 1 Model: "" Number of chains: 10 Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "m" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.57 Number of scatterers: 8377 At special positions: 0 Unit cell: (91.3, 97.9, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1599 8.00 N 1370 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS b 32 " - pdb=" SG CYS a 32 " distance=2.14 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.04 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.03 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.04 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.04 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 21 sheets defined 25.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'b' and resid 29 through 53 removed outlier: 3.529A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU b 46 " --> pdb=" O TYR b 42 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 102 through 124 removed outlier: 4.496A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.709A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 104 through 108' Processing helix chain 'e' and resid 127 through 154 removed outlier: 3.608A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.599A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 104 through 108' Processing helix chain 'f' and resid 128 through 154 removed outlier: 4.551A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 138 removed outlier: 4.055A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY g 138 " --> pdb=" O TYR g 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.818A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 106' Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.573A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 272 removed outlier: 3.846A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.949A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 158 removed outlier: 3.755A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 217 through 221 Processing helix chain 'n' and resid 270 through 308 removed outlier: 4.452A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.434A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 5.977A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.851A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 39 through 40 removed outlier: 3.551A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 40 removed outlier: 3.513A pdb=" N VAL f 45 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 65 through 66 removed outlier: 3.514A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 111 through 117 removed outlier: 6.875A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.641A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 60 through 65 removed outlier: 3.583A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 40 through 46 removed outlier: 3.626A pdb=" N ILE m 98 " --> pdb=" O VAL m 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU m 96 " --> pdb=" O LEU m 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR m 93 " --> pdb=" O ASP m 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN m 86 " --> pdb=" O SER m 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.519A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 180 through 184 removed outlier: 3.549A pdb=" N THR m 180 " --> pdb=" O SER m 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU m 182 " --> pdb=" O SER m 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE m 189 " --> pdb=" O MET m 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 29 through 33 removed outlier: 3.588A pdb=" N THR n 131 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR n 133 " --> pdb=" O LEU n 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 38 through 40 removed outlier: 3.800A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 73 through 76 removed outlier: 7.348A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER n 52 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 183 through 184 removed outlier: 3.619A pdb=" N LYS n 183 " --> pdb=" O VAL n 180 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 972 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: 2.37 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2281 1.33 - 1.46: 2075 1.46 - 1.58: 4126 1.58 - 1.71: 3 1.71 - 1.83: 76 Bond restraints: 8561 Sorted by residual: bond pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.467 1.644 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" O3 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.467 1.632 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C SER f 103 " pdb=" N LYS f 104 " ideal model delta sigma weight residual 1.331 1.220 0.111 2.07e-02 2.33e+03 2.88e+01 bond pdb=" O6 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.637 1.536 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O6 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.637 1.545 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 8556 not shown) Histogram of bond angle deviations from ideal: 83.64 - 93.75: 3 93.75 - 103.87: 123 103.87 - 113.98: 4906 113.98 - 124.10: 6294 124.10 - 134.21: 298 Bond angle restraints: 11624 Sorted by residual: angle pdb=" O2 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 114.52 83.64 30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 113.45 84.47 28.98 3.00e+00 1.11e-01 9.33e+01 angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.01 -15.67 2.08e+00 2.31e-01 5.67e+01 angle pdb=" O4 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O6 C3S m1001 " ideal model delta sigma weight residual 105.67 84.46 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" CG LYS b 30 " pdb=" CD LYS b 30 " pdb=" CE LYS b 30 " ideal model delta sigma weight residual 111.30 126.51 -15.21 2.30e+00 1.89e-01 4.37e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 4844 16.50 - 33.00: 278 33.00 - 49.50: 82 49.50 - 66.00: 21 66.00 - 82.50: 10 Dihedral angle restraints: 5235 sinusoidal: 2159 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA MET g 103 " pdb=" C MET g 103 " pdb=" N CYS g 104 " pdb=" CA CYS g 104 " ideal model delta harmonic sigma weight residual -180.00 -134.18 -45.82 0 5.00e+00 4.00e-02 8.40e+01 ... (remaining 5232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1100 0.094 - 0.189: 194 0.189 - 0.283: 11 0.283 - 0.377: 2 0.377 - 0.472: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU d 29 " pdb=" CB LEU d 29 " pdb=" CD1 LEU d 29 " pdb=" CD2 LEU d 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1305 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO n 223 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.13e-02 9.08e+00 pdb=" CG TYR d 90 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN m 102 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO m 103 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO m 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO m 103 " -0.040 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1730 2.78 - 3.31: 6761 3.31 - 3.84: 12261 3.84 - 4.37: 13401 4.37 - 4.90: 24676 Nonbonded interactions: 58829 Sorted by model distance: nonbonded pdb=" O VAL f 148 " pdb=" OG SER f 152 " model vdw 2.256 2.440 nonbonded pdb=" NH2 ARG m 253 " pdb=" OD1 ASP a 36 " model vdw 2.258 2.520 nonbonded pdb=" NE1 TRP m 271 " pdb=" O4 C3S m1001 " model vdw 2.289 2.520 nonbonded pdb=" OE1 GLN d 94 " pdb=" OG SER a 23 " model vdw 2.292 2.440 nonbonded pdb=" O TYR e 149 " pdb=" OG SER e 152 " model vdw 2.318 2.440 ... (remaining 58824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 54)) selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } 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 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: 0.920 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: 4.070 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.010 0.177 8561 Z= 0.677 Angle : 1.345 30.884 11624 Z= 0.702 Chirality : 0.070 0.472 1308 Planarity : 0.008 0.075 1468 Dihedral : 12.223 75.568 3222 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.94 % Favored : 90.77 % Rotamer: Outliers : 1.73 % Allowed : 5.29 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -3.59 (0.21), residues: 1040 helix: -1.06 (0.29), residues: 229 sheet: -1.40 (0.30), residues: 277 loop : -3.68 (0.19), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP n 179 HIS 0.017 0.004 HIS n 173 PHE 0.040 0.004 PHE m 157 TYR 0.051 0.005 TYR d 90 ARG 0.018 0.002 ARG m 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.010 Fit side-chains REVERT: b 39 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7845 (mp) REVERT: b 54 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.5059 (tttm) REVERT: d 27 GLU cc_start: 0.7935 (pt0) cc_final: 0.7688 (pt0) REVERT: d 56 THR cc_start: 0.8023 (p) cc_final: 0.7796 (p) REVERT: e 74 ASN cc_start: 0.8041 (m-40) cc_final: 0.7730 (m-40) REVERT: e 85 LYS cc_start: 0.8654 (mttt) cc_final: 0.8441 (mmtt) REVERT: e 124 GLU cc_start: 0.7486 (tt0) cc_final: 0.6965 (tt0) REVERT: e 128 MET cc_start: 0.7294 (mmm) cc_final: 0.7080 (mmm) REVERT: f 51 GLN cc_start: 0.6480 (mt0) cc_final: 0.5822 (mp10) REVERT: f 83 SER cc_start: 0.8253 (m) cc_final: 0.7960 (p) REVERT: g 30 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7167 (pp) REVERT: m 104 SER cc_start: 0.7053 (m) cc_final: 0.6531 (p) REVERT: m 145 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7048 (ttm110) REVERT: m 184 MET cc_start: 0.8549 (ptm) cc_final: 0.8308 (ptm) REVERT: n 80 PRO cc_start: 0.7073 (Cg_endo) cc_final: 0.6721 (Cg_exo) REVERT: n 261 ARG cc_start: 0.7142 (ppt-90) cc_final: 0.6680 (ptt180) outliers start: 16 outliers final: 1 residues processed: 196 average time/residue: 0.2266 time to fit residues: 58.9108 Evaluate side-chains 121 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain g residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN f 60 GLN f 65 ASN g 29 HIS m 102 GLN n 25 GLN n 47 ASN ** n 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8561 Z= 0.196 Angle : 0.653 8.069 11624 Z= 0.341 Chirality : 0.044 0.197 1308 Planarity : 0.005 0.046 1468 Dihedral : 6.756 53.956 1289 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.16 % Allowed : 9.39 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.82 (0.25), residues: 1040 helix: 1.71 (0.33), residues: 244 sheet: -0.48 (0.31), residues: 290 loop : -3.32 (0.21), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 43 HIS 0.003 0.001 HIS d 89 PHE 0.025 0.002 PHE m 157 TYR 0.022 0.002 TYR n 50 ARG 0.005 0.001 ARG n 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.017 Fit side-chains REVERT: e 86 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7715 (mt-10) REVERT: e 125 MET cc_start: 0.8138 (mmt) cc_final: 0.7792 (mmt) REVERT: e 128 MET cc_start: 0.6849 (mmm) cc_final: 0.6584 (mmt) REVERT: f 111 TYR cc_start: 0.8372 (m-10) cc_final: 0.8106 (m-80) REVERT: g 30 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7146 (mp) REVERT: g 77 ASN cc_start: 0.8081 (p0) cc_final: 0.7828 (p0) REVERT: m 104 SER cc_start: 0.7382 (m) cc_final: 0.6878 (p) REVERT: m 145 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7060 (ttm110) REVERT: m 185 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7656 (mtm-85) REVERT: n 80 PRO cc_start: 0.7058 (Cg_endo) cc_final: 0.6678 (Cg_exo) REVERT: n 261 ARG cc_start: 0.7621 (ppt-90) cc_final: 0.7055 (ptt180) outliers start: 20 outliers final: 4 residues processed: 161 average time/residue: 0.2553 time to fit residues: 53.4620 Evaluate side-chains 126 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain n residue 68 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN g 105 GLN n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8561 Z= 0.213 Angle : 0.649 9.051 11624 Z= 0.337 Chirality : 0.044 0.217 1308 Planarity : 0.005 0.043 1468 Dihedral : 6.174 48.937 1281 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 3.34 % Allowed : 11.76 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1040 helix: 2.62 (0.33), residues: 244 sheet: 0.05 (0.33), residues: 280 loop : -2.96 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 43 HIS 0.006 0.001 HIS n 66 PHE 0.019 0.002 PHE n 29 TYR 0.019 0.002 TYR g 34 ARG 0.006 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.878 Fit side-chains REVERT: d 27 GLU cc_start: 0.8110 (pt0) cc_final: 0.7873 (pt0) REVERT: e 37 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7916 (mttp) REVERT: e 85 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8618 (mttp) REVERT: e 86 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7757 (mt-10) REVERT: g 30 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (pp) REVERT: g 77 ASN cc_start: 0.8348 (p0) cc_final: 0.7912 (p0) REVERT: m 145 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7252 (ttm110) REVERT: n 80 PRO cc_start: 0.7058 (Cg_endo) cc_final: 0.6761 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: n 261 ARG cc_start: 0.8082 (ppt-90) cc_final: 0.7632 (ptt180) outliers start: 31 outliers final: 14 residues processed: 157 average time/residue: 0.2269 time to fit residues: 47.7627 Evaluate side-chains 135 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 44 ASN Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 158 THR Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 60 GLN g 105 GLN n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8561 Z= 0.208 Angle : 0.616 9.146 11624 Z= 0.319 Chirality : 0.043 0.172 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.961 51.770 1281 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 3.34 % Allowed : 12.19 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.64 (0.26), residues: 1040 helix: 3.05 (0.32), residues: 242 sheet: 0.24 (0.32), residues: 297 loop : -2.82 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.014 0.002 PHE m 157 TYR 0.017 0.002 TYR n 50 ARG 0.003 0.000 ARG m 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8031 (pt0) cc_final: 0.7764 (pt0) REVERT: d 82 LYS cc_start: 0.7632 (mttt) cc_final: 0.7370 (mttt) REVERT: d 99 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6560 (pp) REVERT: e 37 LYS cc_start: 0.8450 (mmtt) cc_final: 0.7926 (mttp) REVERT: e 85 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8560 (mttp) REVERT: e 86 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7717 (mt-10) REVERT: f 104 LYS cc_start: 0.8730 (tttt) cc_final: 0.8061 (mttt) REVERT: g 58 ASP cc_start: 0.8091 (m-30) cc_final: 0.7820 (m-30) REVERT: g 77 ASN cc_start: 0.8457 (p0) cc_final: 0.7861 (p0) REVERT: g 92 ASN cc_start: 0.7020 (m110) cc_final: 0.5965 (t0) REVERT: m 121 THR cc_start: 0.7174 (m) cc_final: 0.6695 (p) REVERT: m 145 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7154 (ttm110) REVERT: m 148 LYS cc_start: 0.7036 (mptt) cc_final: 0.6770 (mttt) REVERT: m 230 LYS cc_start: 0.8473 (mttt) cc_final: 0.8252 (mmtt) REVERT: n 32 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (pp) REVERT: n 50 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.4870 (p90) REVERT: n 80 PRO cc_start: 0.7304 (Cg_endo) cc_final: 0.7006 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: n 261 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7853 (ptt180) outliers start: 31 outliers final: 17 residues processed: 158 average time/residue: 0.2083 time to fit residues: 44.8340 Evaluate side-chains 145 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain m residue 158 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 105 GLN n 25 GLN n 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8561 Z= 0.171 Angle : 0.589 9.073 11624 Z= 0.303 Chirality : 0.042 0.202 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.624 51.833 1279 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 3.13 % Allowed : 12.94 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.32 (0.27), residues: 1040 helix: 3.66 (0.32), residues: 235 sheet: 0.38 (0.33), residues: 289 loop : -2.64 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.002 0.001 HIS n 66 PHE 0.014 0.001 PHE m 157 TYR 0.013 0.001 TYR n 50 ARG 0.003 0.000 ARG m 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8013 (pt0) cc_final: 0.7774 (pt0) REVERT: d 82 LYS cc_start: 0.7654 (mttt) cc_final: 0.7407 (mttt) REVERT: d 99 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6624 (pp) REVERT: e 37 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7924 (mttp) REVERT: e 85 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8558 (mttp) REVERT: e 86 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7706 (mt-10) REVERT: f 104 LYS cc_start: 0.8835 (tttt) cc_final: 0.8150 (mttt) REVERT: g 77 ASN cc_start: 0.8405 (p0) cc_final: 0.7785 (p0) REVERT: g 92 ASN cc_start: 0.7043 (m110) cc_final: 0.5930 (t0) REVERT: m 145 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7027 (ttm110) REVERT: m 230 LYS cc_start: 0.8443 (mttt) cc_final: 0.8240 (mmtt) REVERT: n 28 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7316 (mtmm) REVERT: n 50 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.4984 (p90) REVERT: n 80 PRO cc_start: 0.7365 (Cg_endo) cc_final: 0.7093 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8233 (tt) REVERT: n 252 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: n 261 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (ptt180) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2179 time to fit residues: 42.9445 Evaluate side-chains 144 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 44 ASN Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8561 Z= 0.159 Angle : 0.571 8.783 11624 Z= 0.293 Chirality : 0.041 0.166 1308 Planarity : 0.004 0.028 1468 Dihedral : 5.497 54.862 1279 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.67 % Allowed : 12.84 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.27), residues: 1040 helix: 3.95 (0.31), residues: 235 sheet: 0.51 (0.33), residues: 285 loop : -2.51 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.002 0.001 HIS n 226 PHE 0.011 0.001 PHE m 157 TYR 0.013 0.001 TYR n 50 ARG 0.004 0.000 ARG m 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8036 (pt0) cc_final: 0.7765 (pt0) REVERT: d 82 LYS cc_start: 0.7668 (mttt) cc_final: 0.7418 (mttt) REVERT: d 99 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6597 (pp) REVERT: d 123 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6086 (t80) REVERT: e 37 LYS cc_start: 0.8465 (mmtt) cc_final: 0.7923 (mttp) REVERT: e 85 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8547 (mttp) REVERT: e 86 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7719 (mt-10) REVERT: f 104 LYS cc_start: 0.8876 (tttt) cc_final: 0.8122 (mttt) REVERT: g 77 ASN cc_start: 0.8411 (p0) cc_final: 0.7852 (p0) REVERT: g 92 ASN cc_start: 0.7272 (m110) cc_final: 0.5930 (t0) REVERT: g 106 ASN cc_start: 0.7593 (m-40) cc_final: 0.7322 (m-40) REVERT: m 145 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7002 (ttm110) REVERT: n 28 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7316 (mtmm) REVERT: n 32 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (pp) REVERT: n 50 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4868 (p90) REVERT: n 80 PRO cc_start: 0.7386 (Cg_endo) cc_final: 0.7165 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8244 (tt) REVERT: n 252 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: n 261 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (ptt180) outliers start: 34 outliers final: 24 residues processed: 151 average time/residue: 0.2126 time to fit residues: 43.3594 Evaluate side-chains 153 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8561 Z= 0.222 Angle : 0.623 9.219 11624 Z= 0.319 Chirality : 0.043 0.198 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.719 54.411 1279 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 3.78 % Allowed : 13.16 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.16 (0.27), residues: 1040 helix: 3.79 (0.31), residues: 236 sheet: 0.55 (0.34), residues: 275 loop : -2.51 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.013 0.001 PHE f 87 TYR 0.014 0.001 TYR g 34 ARG 0.003 0.000 ARG n 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8139 (pt0) cc_final: 0.7838 (pt0) REVERT: d 82 LYS cc_start: 0.7702 (mttt) cc_final: 0.7451 (mttt) REVERT: d 84 SER cc_start: 0.8622 (p) cc_final: 0.8198 (t) REVERT: d 99 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6743 (pp) REVERT: e 37 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7973 (mttp) REVERT: e 85 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8518 (mttp) REVERT: e 86 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7701 (mt-10) REVERT: g 77 ASN cc_start: 0.8522 (p0) cc_final: 0.7930 (p0) REVERT: g 92 ASN cc_start: 0.7304 (m110) cc_final: 0.5924 (t0) REVERT: g 106 ASN cc_start: 0.7679 (m-40) cc_final: 0.7422 (m-40) REVERT: n 28 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7426 (mtmm) REVERT: n 32 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8179 (pp) REVERT: n 50 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4716 (p90) REVERT: n 80 PRO cc_start: 0.7423 (Cg_endo) cc_final: 0.7190 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8249 (tt) REVERT: n 252 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: n 261 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (ptt180) REVERT: a 26 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8535 (mt) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 0.2719 time to fit residues: 57.6963 Evaluate side-chains 164 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 296 VAL Chi-restraints excluded: chain n residue 300 VAL Chi-restraints excluded: chain a residue 26 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0370 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8561 Z= 0.141 Angle : 0.553 7.939 11624 Z= 0.284 Chirality : 0.041 0.174 1308 Planarity : 0.003 0.030 1468 Dihedral : 5.405 57.104 1279 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.88 % Allowed : 13.27 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.08 (0.27), residues: 1040 helix: 4.08 (0.31), residues: 236 sheet: 0.62 (0.33), residues: 283 loop : -2.41 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.002 0.000 HIS n 173 PHE 0.011 0.001 PHE m 157 TYR 0.012 0.001 TYR e 52 ARG 0.002 0.000 ARG m 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.7993 (pt0) cc_final: 0.7736 (pt0) REVERT: d 82 LYS cc_start: 0.7742 (mttt) cc_final: 0.7493 (mttt) REVERT: d 99 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6692 (pp) REVERT: d 123 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6477 (t80) REVERT: e 37 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7908 (mttp) REVERT: e 86 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7737 (mt-10) REVERT: g 77 ASN cc_start: 0.8442 (p0) cc_final: 0.7859 (p0) REVERT: g 92 ASN cc_start: 0.7382 (m110) cc_final: 0.5902 (t0) REVERT: g 106 ASN cc_start: 0.7620 (m-40) cc_final: 0.7358 (m-40) REVERT: m 121 THR cc_start: 0.7122 (m) cc_final: 0.6628 (p) REVERT: n 28 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7472 (mtmm) REVERT: n 32 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (pp) REVERT: n 50 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5023 (p90) REVERT: n 80 PRO cc_start: 0.7500 (Cg_endo) cc_final: 0.7281 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8297 (tt) REVERT: n 252 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8092 (pt0) outliers start: 36 outliers final: 24 residues processed: 157 average time/residue: 0.2280 time to fit residues: 48.7239 Evaluate side-chains 157 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 44 ASN Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 68 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.4980 chunk 71 optimal weight: 0.1980 chunk 28 optimal weight: 0.2980 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 91 optimal weight: 0.0010 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 overall best weight: 0.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 8561 Z= 0.122 Angle : 0.524 7.706 11624 Z= 0.268 Chirality : 0.040 0.202 1308 Planarity : 0.003 0.026 1468 Dihedral : 5.087 59.234 1279 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.59 % Allowed : 14.56 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.36 (0.27), residues: 1040 helix: 4.37 (0.31), residues: 237 sheet: 0.77 (0.34), residues: 274 loop : -2.20 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.002 0.000 HIS e 81 PHE 0.013 0.001 PHE n 29 TYR 0.010 0.001 TYR n 50 ARG 0.001 0.000 ARG n 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.7843 (pt0) cc_final: 0.7539 (tt0) REVERT: d 82 LYS cc_start: 0.7734 (mttt) cc_final: 0.7335 (mttt) REVERT: d 99 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6711 (pp) REVERT: e 37 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7864 (mttp) REVERT: e 86 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7696 (mt-10) REVERT: f 86 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7541 (mm-30) REVERT: g 61 MET cc_start: 0.7499 (tpt) cc_final: 0.7220 (tpt) REVERT: g 77 ASN cc_start: 0.8220 (p0) cc_final: 0.7699 (p0) REVERT: g 92 ASN cc_start: 0.7361 (m110) cc_final: 0.6941 (m-40) REVERT: m 121 THR cc_start: 0.6980 (m) cc_final: 0.6538 (p) REVERT: m 159 ASP cc_start: 0.4831 (OUTLIER) cc_final: 0.4550 (p0) REVERT: n 28 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7436 (mtmm) REVERT: n 32 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8232 (pp) REVERT: n 50 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.5015 (p90) REVERT: n 80 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7399 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8159 (tt) REVERT: n 252 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8125 (pt0) outliers start: 24 outliers final: 13 residues processed: 147 average time/residue: 0.2140 time to fit residues: 43.0564 Evaluate side-chains 139 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 150 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 44 ASN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 8561 Z= 0.147 Angle : 0.553 7.762 11624 Z= 0.282 Chirality : 0.041 0.199 1308 Planarity : 0.003 0.026 1468 Dihedral : 5.155 59.803 1279 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 2.37 % Allowed : 14.78 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.27), residues: 1040 helix: 4.30 (0.30), residues: 237 sheet: 0.78 (0.32), residues: 287 loop : -2.18 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.002 0.001 HIS n 226 PHE 0.009 0.001 PHE m 157 TYR 0.012 0.001 TYR n 50 ARG 0.002 0.000 ARG n 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.7909 (pt0) cc_final: 0.7623 (pt0) REVERT: d 82 LYS cc_start: 0.7749 (mttt) cc_final: 0.7334 (mttt) REVERT: d 99 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6714 (pp) REVERT: e 37 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7905 (mttp) REVERT: e 86 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7724 (mt-10) REVERT: f 86 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7554 (mm-30) REVERT: g 77 ASN cc_start: 0.8252 (p0) cc_final: 0.7724 (p0) REVERT: g 92 ASN cc_start: 0.7286 (m110) cc_final: 0.6870 (m-40) REVERT: g 106 ASN cc_start: 0.7504 (m-40) cc_final: 0.7195 (m-40) REVERT: m 121 THR cc_start: 0.6972 (m) cc_final: 0.6522 (p) REVERT: m 159 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4772 (p0) REVERT: n 28 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7448 (mtmm) REVERT: n 32 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8165 (pp) REVERT: n 50 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.4977 (p90) REVERT: n 176 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8213 (tt) REVERT: n 252 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8013 (pt0) outliers start: 22 outliers final: 16 residues processed: 142 average time/residue: 0.2171 time to fit residues: 41.7892 Evaluate side-chains 147 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 150 TYR Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 44 ASN Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137114 restraints weight = 9368.403| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.37 r_work: 0.3069 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8561 Z= 0.167 Angle : 0.568 8.061 11624 Z= 0.289 Chirality : 0.041 0.215 1308 Planarity : 0.004 0.097 1468 Dihedral : 5.252 59.813 1279 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 2.48 % Allowed : 14.89 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.27), residues: 1040 helix: 4.26 (0.30), residues: 237 sheet: 0.80 (0.33), residues: 283 loop : -2.16 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.002 0.001 HIS n 226 PHE 0.010 0.001 PHE f 87 TYR 0.012 0.001 TYR n 50 ARG 0.002 0.000 ARG n 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.23 seconds wall clock time: 39 minutes 23.19 seconds (2363.19 seconds total)