Starting phenix.real_space_refine on Fri Jul 19 16:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/07_2024/7fjd_31618.cif" } resolution = 3.2 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 54 5.16 5 C 5341 2.51 5 N 1368 2.21 5 O 1589 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 ARG 155": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 185": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "m ARG 269": "NH1" <-> "NH2" Residue "n PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-5388/modules/chem_data/mon_lib" Total number of atoms: 8352 Number of models: 1 Model: "" Number of chains: 10 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: "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: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 887 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1923 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2241 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.83, per 1000 atoms: 0.58 Number of scatterers: 8352 At special positions: 0 Unit cell: (89.1, 99, 144.1, 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 54 16.00 O 1589 8.00 N 1368 7.00 C 5341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 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: 2.65 Conformation dependent library (CDL) restraints added in 1.6 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: 18 helices and 18 sheets defined 26.4% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.480A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 removed outlier: 3.685A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR b 47 " --> pdb=" O GLY b 43 " (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 76 through 80 Processing helix chain 'd' and resid 102 through 126 removed outlier: 4.076A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.830A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 4.180A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.967A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.914A 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 142 Processing helix chain 'f' and resid 143 through 154 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: 3.729A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.540A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 273 removed outlier: 4.008A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER m 273 " --> pdb=" O ARG m 269 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.628A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.641A 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 269 through 308 removed outlier: 4.172A pdb=" N GLN n 273 " --> pdb=" O GLU n 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 6.075A 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: 6.842A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE e 66 " --> pdb=" O TRP e 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.656A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.510A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU f 47 " --> pdb=" O LEU f 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY f 76 " --> pdb=" O SER f 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 57 through 61 removed outlier: 3.513A pdb=" N LEU f 114 " --> pdb=" O GLY f 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG f 115 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG g 102 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.616A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.785A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP m 57 " --> pdb=" O LEU m 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 41 through 46 Processing sheet with id=AB3, first strand: chain 'm' and resid 140 through 143 removed outlier: 4.093A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 180 through 184 Processing sheet with id=AB5, first strand: chain 'n' and resid 24 through 26 removed outlier: 3.632A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN n 84 " --> pdb=" O ARG n 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 29 through 33 removed outlier: 6.856A pdb=" N GLN n 30 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR n 133 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU n 32 " --> pdb=" O THR n 133 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 183 through 184 372 hydrogen bonds defined for protein. 1026 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: 2.09 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2067 1.33 - 1.46: 2117 1.46 - 1.58: 4275 1.58 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8535 Sorted by residual: bond pdb=" CG LEU a 27 " pdb=" CD2 LEU a 27 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" N ILE n 253 " pdb=" CA ILE n 253 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N CYS b 32 " pdb=" CA CYS b 32 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.23e+00 bond pdb=" CB ARG e 117 " pdb=" CG ARG e 117 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 ... (remaining 8530 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.85: 189 105.85 - 113.09: 4483 113.09 - 120.32: 3465 120.32 - 127.56: 3378 127.56 - 134.79: 71 Bond angle restraints: 11586 Sorted by residual: angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.79 -12.99 2.44e+00 1.68e-01 2.83e+01 angle pdb=" CA TYR n 50 " pdb=" CB TYR n 50 " pdb=" CG TYR n 50 " ideal model delta sigma weight residual 113.90 123.18 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" N ASP m 159 " pdb=" CA ASP m 159 " pdb=" C ASP m 159 " ideal model delta sigma weight residual 110.42 117.93 -7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" CA LEU m 182 " pdb=" CB LEU m 182 " pdb=" CG LEU m 182 " ideal model delta sigma weight residual 116.30 134.30 -18.00 3.50e+00 8.16e-02 2.65e+01 ... (remaining 11581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4888 17.13 - 34.26: 236 34.26 - 51.39: 70 51.39 - 68.52: 16 68.52 - 85.65: 9 Dihedral angle restraints: 5219 sinusoidal: 2143 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 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 178.65 -85.65 1 1.00e+01 1.00e-02 8.87e+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 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1113 0.095 - 0.191: 181 0.191 - 0.286: 9 0.286 - 0.382: 1 0.382 - 0.477: 1 Chirality restraints: 1305 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 0.48 2.00e-01 2.50e+01 5.69e+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 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1302 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 50 " -0.043 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR n 50 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR n 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR n 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.027 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR e 111 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR d 90 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.002 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1302 2.76 - 3.30: 6821 3.30 - 3.83: 12089 3.83 - 4.37: 13423 4.37 - 4.90: 24896 Nonbonded interactions: 58531 Sorted by model distance: nonbonded pdb=" NZ LYS b 30 " pdb=" O1 CLR b 201 " model vdw 2.229 2.520 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.305 2.520 nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.310 2.440 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.408 2.520 nonbonded pdb=" N ASP g 39 " pdb=" OD1 ASP g 39 " model vdw 2.409 2.520 ... (remaining 58526 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' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 77 or (resid 78 and (nam \ e N or name CA or name C or name O or name CB )) or resid 79 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: 0.680 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.780 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.011 0.120 8535 Z= 0.669 Angle : 1.240 18.002 11586 Z= 0.666 Chirality : 0.068 0.477 1305 Planarity : 0.008 0.073 1466 Dihedral : 11.941 82.404 3206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.87 % Rotamer: Outliers : 0.87 % Allowed : 6.19 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.57 (0.22), residues: 1040 helix: -1.03 (0.28), residues: 237 sheet: -1.35 (0.29), residues: 292 loop : -3.79 (0.19), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP e 59 HIS 0.018 0.005 HIS f 61 PHE 0.041 0.005 PHE f 110 TYR 0.063 0.005 TYR d 90 ARG 0.015 0.002 ARG d 63 *********************** 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 204 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.947 Fit side-chains REVERT: e 41 SER cc_start: 0.9071 (t) cc_final: 0.8756 (p) REVERT: e 57 ILE cc_start: 0.8760 (mp) cc_final: 0.8355 (tt) REVERT: f 117 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8258 (ttm170) REVERT: g 32 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8215 (mptt) REVERT: g 53 ILE cc_start: 0.7888 (mm) cc_final: 0.7685 (mt) REVERT: m 99 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6860 (mtm-85) REVERT: m 173 ASP cc_start: 0.7734 (m-30) cc_final: 0.7082 (p0) REVERT: m 211 ASN cc_start: 0.8609 (t160) cc_final: 0.8401 (t0) REVERT: n 33 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7531 (ptmt) REVERT: n 92 ASP cc_start: 0.7574 (m-30) cc_final: 0.6680 (t70) REVERT: n 96 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7403 (mtt90) REVERT: n 113 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5994 (mtm180) REVERT: n 121 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6581 (mp0) REVERT: n 183 LYS cc_start: 0.7914 (mttt) cc_final: 0.7421 (mtpp) outliers start: 8 outliers final: 1 residues processed: 202 average time/residue: 0.2398 time to fit residues: 62.8184 Evaluate side-chains 135 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN m 136 ASN m 168 GLN n 25 GLN n 47 ASN ** n 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8535 Z= 0.180 Angle : 0.619 8.571 11586 Z= 0.329 Chirality : 0.043 0.218 1305 Planarity : 0.005 0.050 1466 Dihedral : 7.086 55.621 1275 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.04 % Allowed : 8.03 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.25), residues: 1040 helix: 1.72 (0.33), residues: 242 sheet: -0.20 (0.32), residues: 275 loop : -3.40 (0.21), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.004 0.001 HIS f 81 PHE 0.021 0.002 PHE m 157 TYR 0.031 0.002 TYR n 50 ARG 0.002 0.000 ARG b 52 *********************** 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 180 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.892 Fit side-chains REVERT: b 34 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7716 (mt) REVERT: d 99 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6819 (pp) REVERT: e 41 SER cc_start: 0.9045 (t) cc_final: 0.8817 (p) REVERT: e 57 ILE cc_start: 0.8786 (mp) cc_final: 0.8340 (tt) REVERT: e 80 ASP cc_start: 0.8356 (p0) cc_final: 0.8155 (p0) REVERT: f 80 ASP cc_start: 0.7945 (t70) cc_final: 0.7540 (t0) REVERT: f 101 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7507 (tpp-160) REVERT: g 30 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7335 (mp) REVERT: m 173 ASP cc_start: 0.7537 (m-30) cc_final: 0.7016 (p0) REVERT: n 33 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7400 (ptmt) REVERT: n 92 ASP cc_start: 0.7535 (m-30) cc_final: 0.6708 (t70) REVERT: n 96 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7201 (mtt90) REVERT: n 302 MET cc_start: 0.7294 (ttp) cc_final: 0.5680 (mmt) outliers start: 28 outliers final: 15 residues processed: 173 average time/residue: 0.2097 time to fit residues: 48.8008 Evaluate side-chains 144 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 71 LYS Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 95 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 128 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8535 Z= 0.292 Angle : 0.678 10.288 11586 Z= 0.357 Chirality : 0.045 0.203 1305 Planarity : 0.005 0.050 1466 Dihedral : 6.639 48.328 1275 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.15 % Rotamer: Outliers : 4.99 % Allowed : 10.97 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1040 helix: 2.27 (0.33), residues: 241 sheet: 0.18 (0.32), residues: 285 loop : -3.28 (0.21), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 43 HIS 0.008 0.002 HIS n 173 PHE 0.018 0.002 PHE m 157 TYR 0.026 0.002 TYR n 50 ARG 0.004 0.001 ARG e 117 *********************** 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 175 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 0.868 Fit side-chains REVERT: b 34 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7738 (mt) REVERT: d 27 GLU cc_start: 0.7834 (pt0) cc_final: 0.7595 (pt0) REVERT: d 29 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7585 (mm) REVERT: d 99 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6591 (pp) REVERT: d 117 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7248 (tm) REVERT: e 41 SER cc_start: 0.9051 (t) cc_final: 0.8850 (p) REVERT: e 57 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8313 (tt) REVERT: e 80 ASP cc_start: 0.8453 (p0) cc_final: 0.8207 (p0) REVERT: e 144 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7292 (tp) REVERT: f 80 ASP cc_start: 0.7995 (t70) cc_final: 0.7579 (t0) REVERT: f 106 GLU cc_start: 0.8132 (pt0) cc_final: 0.7574 (pt0) REVERT: m 173 ASP cc_start: 0.7686 (m-30) cc_final: 0.7085 (p0) REVERT: n 33 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7519 (ptmt) REVERT: n 46 MET cc_start: 0.4119 (tmm) cc_final: 0.3412 (tmm) REVERT: n 50 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.5657 (p90) REVERT: n 92 ASP cc_start: 0.7573 (m-30) cc_final: 0.6705 (t70) REVERT: n 96 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7247 (mtt90) REVERT: n 121 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6496 (mp0) REVERT: n 252 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7886 (pt0) outliers start: 46 outliers final: 27 residues processed: 161 average time/residue: 0.2072 time to fit residues: 44.8004 Evaluate side-chains 159 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 GLN n 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8535 Z= 0.131 Angle : 0.520 8.801 11586 Z= 0.277 Chirality : 0.041 0.177 1305 Planarity : 0.004 0.042 1466 Dihedral : 5.521 44.990 1275 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.15 % Allowed : 13.79 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 1040 helix: 3.21 (0.32), residues: 241 sheet: 0.40 (0.32), residues: 307 loop : -3.02 (0.22), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 PHE 0.014 0.001 PHE m 157 TYR 0.021 0.001 TYR n 50 ARG 0.002 0.000 ARG b 52 *********************** 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 173 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.7789 (pt0) cc_final: 0.7552 (pt0) REVERT: d 29 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7208 (mm) REVERT: d 99 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6785 (pp) REVERT: d 117 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7169 (tp) REVERT: e 79 GLU cc_start: 0.7687 (pm20) cc_final: 0.7437 (pm20) REVERT: e 104 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7416 (ttpt) REVERT: e 128 MET cc_start: 0.6347 (mmm) cc_final: 0.6123 (mmp) REVERT: e 144 LEU cc_start: 0.7524 (mm) cc_final: 0.7320 (tp) REVERT: f 80 ASP cc_start: 0.7906 (t70) cc_final: 0.7415 (t0) REVERT: f 106 GLU cc_start: 0.7966 (pt0) cc_final: 0.7398 (pt0) REVERT: f 117 ARG cc_start: 0.8286 (ttm170) cc_final: 0.8014 (ttm-80) REVERT: m 113 MET cc_start: 0.7460 (mtt) cc_final: 0.7062 (mtm) REVERT: n 33 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7458 (ptmt) REVERT: n 38 MET cc_start: 0.7534 (tpt) cc_final: 0.7217 (tmm) REVERT: n 50 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.5386 (p90) REVERT: n 92 ASP cc_start: 0.7498 (m-30) cc_final: 0.6629 (t70) REVERT: n 96 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7235 (mtt90) REVERT: n 121 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6511 (mp0) REVERT: n 252 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7937 (pt0) outliers start: 29 outliers final: 15 residues processed: 168 average time/residue: 0.2283 time to fit residues: 50.7392 Evaluate side-chains 151 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8535 Z= 0.202 Angle : 0.581 9.060 11586 Z= 0.303 Chirality : 0.042 0.192 1305 Planarity : 0.004 0.043 1466 Dihedral : 5.454 44.186 1273 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.89 % Allowed : 12.92 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 1040 helix: 3.31 (0.32), residues: 241 sheet: 0.52 (0.32), residues: 299 loop : -2.94 (0.22), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 43 HIS 0.004 0.001 HIS n 173 PHE 0.013 0.002 PHE f 110 TYR 0.024 0.001 TYR n 50 ARG 0.004 0.000 ARG n 261 *********************** 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 177 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: d 29 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7438 (mm) REVERT: d 99 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6617 (pp) REVERT: d 117 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7258 (tp) REVERT: d 123 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5898 (t80) REVERT: e 57 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8215 (tt) REVERT: e 104 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7436 (ttpt) REVERT: e 128 MET cc_start: 0.6646 (mmm) cc_final: 0.6379 (mmp) REVERT: e 144 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7280 (tp) REVERT: f 80 ASP cc_start: 0.8049 (t70) cc_final: 0.7493 (t0) REVERT: f 106 GLU cc_start: 0.7988 (pt0) cc_final: 0.7417 (pt0) REVERT: f 117 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7970 (ttm-80) REVERT: f 123 MET cc_start: 0.7191 (ttt) cc_final: 0.6955 (ttt) REVERT: m 113 MET cc_start: 0.7548 (mtt) cc_final: 0.7091 (mtt) REVERT: n 33 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7447 (ptmt) REVERT: n 50 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5523 (p90) REVERT: n 92 ASP cc_start: 0.7496 (m-30) cc_final: 0.6641 (t70) REVERT: n 96 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7331 (mtt90) REVERT: n 121 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6482 (mp0) REVERT: n 252 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7908 (pt0) outliers start: 45 outliers final: 24 residues processed: 167 average time/residue: 0.2221 time to fit residues: 49.3602 Evaluate side-chains 159 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.0050 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8535 Z= 0.134 Angle : 0.525 8.781 11586 Z= 0.274 Chirality : 0.041 0.173 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.119 42.935 1273 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 14.98 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 1040 helix: 3.74 (0.31), residues: 241 sheet: 0.66 (0.32), residues: 307 loop : -2.82 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.005 0.001 HIS n 173 PHE 0.012 0.001 PHE m 157 TYR 0.021 0.001 TYR n 50 ARG 0.003 0.000 ARG n 261 *********************** 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 172 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: d 29 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (mm) REVERT: d 99 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6696 (pp) REVERT: d 117 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7261 (tp) REVERT: d 123 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.5867 (t80) REVERT: e 104 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7423 (ttpt) REVERT: e 128 MET cc_start: 0.6390 (mmm) cc_final: 0.6173 (mmp) REVERT: e 144 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7227 (tp) REVERT: f 80 ASP cc_start: 0.7972 (t70) cc_final: 0.7403 (t0) REVERT: f 106 GLU cc_start: 0.7732 (pt0) cc_final: 0.6949 (pt0) REVERT: f 117 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7979 (ttm-80) REVERT: g 43 LEU cc_start: 0.8793 (mp) cc_final: 0.8572 (mm) REVERT: g 52 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.5650 (t0) REVERT: m 113 MET cc_start: 0.7491 (mtt) cc_final: 0.7101 (mtm) REVERT: n 33 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7490 (ptmt) REVERT: n 50 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5542 (p90) REVERT: n 92 ASP cc_start: 0.7480 (m-30) cc_final: 0.6644 (t70) REVERT: n 121 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6423 (mp0) REVERT: n 252 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7958 (pt0) outliers start: 34 outliers final: 20 residues processed: 162 average time/residue: 0.2255 time to fit residues: 48.7149 Evaluate side-chains 158 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 98 optimal weight: 0.0470 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 207 ASN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8535 Z= 0.183 Angle : 0.561 8.797 11586 Z= 0.292 Chirality : 0.042 0.196 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.229 42.661 1273 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.89 % Allowed : 13.79 % Favored : 81.32 % 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: -0.12 (0.27), residues: 1040 helix: 3.73 (0.31), residues: 241 sheet: 0.70 (0.32), residues: 301 loop : -2.76 (0.23), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS n 173 PHE 0.011 0.001 PHE f 110 TYR 0.024 0.001 TYR n 50 ARG 0.004 0.000 ARG n 261 *********************** 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 171 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: d 29 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7462 (mm) REVERT: d 99 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6565 (pp) REVERT: d 117 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7280 (tp) REVERT: d 123 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5752 (t80) REVERT: e 57 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8328 (tt) REVERT: e 104 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7406 (ttpt) REVERT: e 128 MET cc_start: 0.6576 (mmm) cc_final: 0.6323 (mmp) REVERT: e 144 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7290 (tp) REVERT: f 80 ASP cc_start: 0.8030 (t70) cc_final: 0.7462 (t0) REVERT: f 117 ARG cc_start: 0.8270 (ttm170) cc_final: 0.8028 (ttm-80) REVERT: f 123 MET cc_start: 0.7256 (ttt) cc_final: 0.6997 (ttt) REVERT: g 52 ASN cc_start: 0.6146 (OUTLIER) cc_final: 0.5680 (t0) REVERT: m 113 MET cc_start: 0.7384 (mtt) cc_final: 0.7060 (mtm) REVERT: m 143 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: n 33 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7489 (ptmt) REVERT: n 50 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5460 (p90) REVERT: n 92 ASP cc_start: 0.7489 (m-30) cc_final: 0.6639 (t70) REVERT: n 121 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6472 (mp0) REVERT: n 252 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7929 (pt0) outliers start: 45 outliers final: 28 residues processed: 157 average time/residue: 0.2136 time to fit residues: 45.1254 Evaluate side-chains 163 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8535 Z= 0.153 Angle : 0.533 8.878 11586 Z= 0.278 Chirality : 0.041 0.176 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.092 42.046 1273 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.13 % Allowed : 14.44 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 1040 helix: 3.89 (0.30), residues: 241 sheet: 0.77 (0.33), residues: 301 loop : -2.66 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS n 173 PHE 0.011 0.001 PHE m 157 TYR 0.022 0.001 TYR n 50 ARG 0.003 0.000 ARG n 261 *********************** 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 168 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: d 29 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7325 (mm) REVERT: d 99 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6535 (pp) REVERT: d 117 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7276 (tp) REVERT: d 123 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5657 (t80) REVERT: e 104 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7407 (ttpt) REVERT: e 144 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7164 (tp) REVERT: f 80 ASP cc_start: 0.7985 (t70) cc_final: 0.7390 (t0) REVERT: f 117 ARG cc_start: 0.8259 (ttm170) cc_final: 0.8029 (ttm-80) REVERT: f 123 MET cc_start: 0.7288 (ttt) cc_final: 0.7029 (ttt) REVERT: g 43 LEU cc_start: 0.8847 (mt) cc_final: 0.8584 (mp) REVERT: g 52 ASN cc_start: 0.6111 (OUTLIER) cc_final: 0.5646 (t0) REVERT: m 113 MET cc_start: 0.7225 (mtt) cc_final: 0.6987 (mtm) REVERT: n 33 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7467 (ptmt) REVERT: n 50 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5458 (p90) REVERT: n 92 ASP cc_start: 0.7478 (m-30) cc_final: 0.6637 (t70) REVERT: n 121 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6452 (mp0) REVERT: n 252 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7952 (pt0) outliers start: 38 outliers final: 28 residues processed: 157 average time/residue: 0.2213 time to fit residues: 46.6154 Evaluate side-chains 162 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8535 Z= 0.166 Angle : 0.542 8.760 11586 Z= 0.283 Chirality : 0.041 0.184 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.111 41.972 1273 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.45 % Allowed : 14.66 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1040 helix: 3.91 (0.30), residues: 241 sheet: 0.80 (0.32), residues: 307 loop : -2.66 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS n 173 PHE 0.011 0.001 PHE f 110 TYR 0.023 0.001 TYR n 50 ARG 0.005 0.000 ARG n 261 *********************** 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 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6628 (pp) REVERT: d 117 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7277 (tp) REVERT: d 123 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5574 (t80) REVERT: e 57 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8389 (tt) REVERT: e 90 LEU cc_start: 0.8463 (tp) cc_final: 0.8218 (tp) REVERT: e 104 LYS cc_start: 0.7923 (mmtp) cc_final: 0.7415 (ttpt) REVERT: e 123 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7389 (ptp) REVERT: e 144 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7153 (tp) REVERT: f 80 ASP cc_start: 0.8003 (t70) cc_final: 0.7413 (t0) REVERT: f 117 ARG cc_start: 0.8263 (ttm170) cc_final: 0.8044 (ttm-80) REVERT: g 43 LEU cc_start: 0.8871 (mt) cc_final: 0.8592 (mp) REVERT: g 52 ASN cc_start: 0.6125 (OUTLIER) cc_final: 0.5693 (t0) REVERT: m 113 MET cc_start: 0.7173 (mtt) cc_final: 0.6943 (mtm) REVERT: n 33 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7465 (ptmt) REVERT: n 38 MET cc_start: 0.7554 (tpt) cc_final: 0.7321 (tmm) REVERT: n 50 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5422 (p90) REVERT: n 92 ASP cc_start: 0.7513 (m-30) cc_final: 0.6667 (t70) REVERT: n 121 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6458 (mp0) REVERT: n 252 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7929 (pt0) outliers start: 41 outliers final: 29 residues processed: 152 average time/residue: 0.2312 time to fit residues: 47.0333 Evaluate side-chains 163 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5691 > 50: distance: 25 - 63: 13.848 distance: 28 - 60: 18.970 distance: 50 - 54: 19.016 distance: 54 - 55: 29.111 distance: 55 - 56: 20.167 distance: 55 - 58: 10.058 distance: 56 - 57: 8.351 distance: 56 - 60: 16.498 distance: 58 - 59: 21.879 distance: 60 - 61: 23.894 distance: 61 - 62: 24.072 distance: 61 - 64: 21.760 distance: 62 - 63: 13.611 distance: 62 - 68: 8.239 distance: 64 - 65: 11.523 distance: 65 - 66: 4.430 distance: 66 - 67: 14.691 distance: 69 - 70: 14.109 distance: 70 - 71: 11.018 distance: 70 - 77: 17.582 distance: 72 - 73: 21.667 distance: 73 - 74: 5.596 distance: 74 - 75: 11.058 distance: 74 - 76: 11.521 distance: 77 - 78: 5.232 distance: 78 - 79: 10.302 distance: 78 - 81: 6.611 distance: 79 - 80: 14.357 distance: 79 - 85: 13.536 distance: 81 - 82: 10.987 distance: 82 - 83: 14.318 distance: 83 - 84: 13.818 distance: 85 - 86: 16.640 distance: 86 - 87: 10.870 distance: 86 - 89: 10.595 distance: 87 - 88: 4.547 distance: 87 - 93: 9.262 distance: 89 - 90: 19.031 distance: 90 - 91: 13.271 distance: 90 - 92: 23.077 distance: 93 - 94: 9.640 distance: 94 - 95: 8.559 distance: 94 - 97: 18.075 distance: 95 - 96: 13.652 distance: 95 - 100: 16.296 distance: 97 - 98: 3.884 distance: 97 - 99: 3.252 distance: 100 - 101: 13.260 distance: 101 - 102: 5.643 distance: 101 - 104: 14.847 distance: 102 - 103: 10.922 distance: 102 - 108: 6.687 distance: 103 - 126: 17.606 distance: 104 - 105: 6.421 distance: 105 - 106: 13.401 distance: 106 - 107: 11.325 distance: 108 - 109: 12.032 distance: 109 - 110: 13.721 distance: 109 - 112: 12.102 distance: 110 - 111: 8.069 distance: 110 - 114: 11.574 distance: 111 - 133: 13.286 distance: 112 - 113: 15.223 distance: 114 - 115: 9.648 distance: 115 - 116: 10.099 distance: 115 - 118: 4.631 distance: 116 - 117: 18.418 distance: 116 - 121: 3.882 distance: 117 - 141: 24.790 distance: 118 - 119: 6.744 distance: 118 - 120: 17.488 distance: 121 - 122: 6.246 distance: 122 - 123: 9.118 distance: 122 - 125: 23.686 distance: 123 - 124: 9.140 distance: 123 - 126: 3.072 distance: 124 - 147: 9.673