Starting phenix.real_space_refine on Thu Feb 15 13:40:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/02_2024/8uhf_42279.pdb" } resolution = 3.8 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= 0.121 sd= 0.873 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 61 5.16 5 C 7833 2.51 5 N 2083 2.21 5 O 2434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12411 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1369 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1413 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1413 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1369 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "E" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1358 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 184} Chain breaks: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1370 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "G" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1413 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 191} Chain: "H" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1345 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1361 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Time building chain proxies: 7.04, per 1000 atoms: 0.57 Number of scatterers: 12411 At special positions: 0 Unit cell: (96.28, 96.28, 158.53, 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 61 16.00 O 2434 8.00 N 2083 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 186 " distance=2.04 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS F 120 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 120 " - pdb=" SG CYS G 186 " distance=2.03 Simple disulfide: pdb=" SG CYS H 120 " - pdb=" SG CYS H 186 " distance=2.03 Simple disulfide: pdb=" SG CYS I 120 " - pdb=" SG CYS I 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 45.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 19 through 51 removed outlier: 4.120A pdb=" N SER A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.525A pdb=" N ILE B 7 " --> pdb=" O LEU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 51 removed outlier: 3.571A pdb=" N SER B 17 " --> pdb=" O MET B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 116 through 128 removed outlier: 3.781A pdb=" N LYS B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'C' and resid 3 through 52 removed outlier: 4.059A pdb=" N VAL C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 19 through 51 removed outlier: 4.081A pdb=" N LEU D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 51 Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'F' and resid 3 through 51 removed outlier: 3.646A pdb=" N ILE F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 Processing helix chain 'F' and resid 80 through 85 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 143 through 147 Processing helix chain 'F' and resid 178 through 184 Processing helix chain 'G' and resid 2 through 51 removed outlier: 3.989A pdb=" N GLY G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 178 through 184 removed outlier: 3.562A pdb=" N VAL G 182 " --> pdb=" O ASN G 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 49 removed outlier: 3.580A pdb=" N ILE H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL H 16 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 178 through 184 Processing helix chain 'I' and resid 4 through 19 removed outlier: 3.917A pdb=" N ILE I 8 " --> pdb=" O LEU I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 51 Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 178 through 184 removed outlier: 3.644A pdb=" N VAL I 182 " --> pdb=" O ASN I 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 6.176A pdb=" N PHE A 192 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 94 through 96 removed outlier: 6.660A pdb=" N ILE B 134 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.614A pdb=" N ASN C 94 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 134 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 100 removed outlier: 6.524A pdb=" N ARG D 100 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN D 105 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER D 111 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE D 196 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASP D 113 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 194 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 134 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.983A pdb=" N PHE E 108 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 134 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.729A pdb=" N ASN F 94 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 107 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA F 109 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN F 198 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER F 111 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE F 196 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP F 113 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 194 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 134 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 94 through 100 removed outlier: 7.028A pdb=" N ARG G 100 " --> pdb=" O ASN G 105 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN G 105 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE G 192 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 133 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE G 134 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 94 through 100 removed outlier: 7.078A pdb=" N ARG H 100 " --> pdb=" O ASN H 105 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN H 105 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE H 108 " --> pdb=" O ASN H 198 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE H 192 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR H 133 " --> pdb=" O GLY H 197 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE H 134 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 94 through 98 removed outlier: 3.510A pdb=" N ALA I 107 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA I 109 " --> pdb=" O ASN I 198 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN I 198 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER I 111 " --> pdb=" O PHE I 196 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE I 196 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP I 113 " --> pdb=" O VAL I 194 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL I 194 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR I 133 " --> pdb=" O GLY I 197 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE I 134 " --> pdb=" O ILE I 164 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4098 1.34 - 1.46: 2512 1.46 - 1.58: 5823 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 12537 Sorted by residual: bond pdb=" CG PRO G 191 " pdb=" CD PRO G 191 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.45e-01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.24e-01 bond pdb=" CB CYS E 120 " pdb=" SG CYS E 120 " ideal model delta sigma weight residual 1.808 1.781 0.027 3.30e-02 9.18e+02 6.89e-01 bond pdb=" C VAL D 127 " pdb=" O VAL D 127 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.15e-01 bond pdb=" CG PRO E 191 " pdb=" CD PRO E 191 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 5.96e-01 ... (remaining 12532 not shown) Histogram of bond angle deviations from ideal: 99.55 - 105.48: 201 105.48 - 111.41: 5817 111.41 - 117.34: 3475 117.34 - 123.27: 7228 123.27 - 129.21: 280 Bond angle restraints: 17001 Sorted by residual: angle pdb=" CA CYS C 120 " pdb=" CB CYS C 120 " pdb=" SG CYS C 120 " ideal model delta sigma weight residual 114.40 123.32 -8.92 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N ILE B 7 " pdb=" CA ILE B 7 " pdb=" C ILE B 7 " ideal model delta sigma weight residual 112.80 108.83 3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C LEU C 185 " pdb=" N CYS C 186 " pdb=" CA CYS C 186 " ideal model delta sigma weight residual 122.46 126.59 -4.13 1.41e+00 5.03e-01 8.56e+00 angle pdb=" C LEU A 3 " pdb=" N LEU A 4 " pdb=" CA LEU A 4 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.08e+00 angle pdb=" C CYS C 120 " pdb=" CA CYS C 120 " pdb=" CB CYS C 120 " ideal model delta sigma weight residual 110.84 106.92 3.92 1.66e+00 3.63e-01 5.56e+00 ... (remaining 16996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7104 17.91 - 35.81: 410 35.81 - 53.72: 60 53.72 - 71.63: 15 71.63 - 89.53: 10 Dihedral angle restraints: 7599 sinusoidal: 2686 harmonic: 4913 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 186 " pdb=" CB CYS A 186 " ideal model delta sinusoidal sigma weight residual -86.00 -136.43 50.43 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 120 " pdb=" SG CYS C 120 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual 93.00 129.75 -36.75 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS I 120 " pdb=" SG CYS I 120 " pdb=" SG CYS I 186 " pdb=" CB CYS I 186 " ideal model delta sinusoidal sigma weight residual 93.00 126.56 -33.56 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 7596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1280 0.026 - 0.052: 542 0.052 - 0.078: 206 0.078 - 0.105: 68 0.105 - 0.131: 47 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA ILE G 134 " pdb=" N ILE G 134 " pdb=" C ILE G 134 " pdb=" CB ILE G 134 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL E 112 " pdb=" N VAL E 112 " pdb=" C VAL E 112 " pdb=" CB VAL E 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE E 110 " pdb=" N ILE E 110 " pdb=" C ILE E 110 " pdb=" CB ILE E 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2140 not shown) Planarity restraints: 2174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 4 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C LEU A 4 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 4 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 5 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 9 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C VAL D 9 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 10 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 7 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C ILE B 7 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE B 7 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 2171 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 232 2.68 - 3.24: 12801 3.24 - 3.79: 19679 3.79 - 4.35: 25879 4.35 - 4.90: 42002 Nonbonded interactions: 100593 Sorted by model distance: nonbonded pdb=" OG SER B 39 " pdb=" O GLU B 83 " model vdw 2.126 2.440 nonbonded pdb=" OG SER A 39 " pdb=" O GLU A 83 " model vdw 2.202 2.440 nonbonded pdb=" OG SER F 80 " pdb=" OD1 ASP F 82 " model vdw 2.218 2.440 nonbonded pdb=" O ASP H 149 " pdb=" OG SER H 153 " model vdw 2.240 2.440 nonbonded pdb=" O GLY E 128 " pdb=" NZ LYS E 165 " model vdw 2.247 2.520 ... (remaining 100588 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 2 through 52 or resid 62 through 196)) selection = (chain 'B' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'C' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'D' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'E' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'F' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'G' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'H' and resid 2 through 196) selection = (chain 'I' and (resid 2 through 52 or resid 62 through 196)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 4.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.580 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.002 0.029 12537 Z= 0.122 Angle : 0.495 8.924 17001 Z= 0.277 Chirality : 0.038 0.131 2143 Planarity : 0.003 0.029 2174 Dihedral : 12.209 89.532 4404 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1709 helix: -0.07 (0.18), residues: 733 sheet: -0.81 (0.33), residues: 212 loop : -1.95 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE G 108 TYR 0.004 0.001 TYR G 133 ARG 0.002 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 TYR cc_start: 0.8019 (t80) cc_final: 0.7722 (t80) REVERT: B 165 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8277 (ttpp) REVERT: B 175 ASP cc_start: 0.8310 (m-30) cc_final: 0.7924 (m-30) REVERT: C 25 GLN cc_start: 0.8879 (tp40) cc_final: 0.8429 (tp40) REVERT: C 120 CYS cc_start: 0.4546 (m) cc_final: 0.3447 (m) REVERT: C 129 ASP cc_start: 0.9017 (p0) cc_final: 0.8644 (p0) REVERT: C 131 PHE cc_start: 0.7036 (m-80) cc_final: 0.6806 (m-80) REVERT: C 192 PHE cc_start: 0.5943 (m-80) cc_final: 0.4288 (m-10) REVERT: D 13 MET cc_start: 0.8918 (mmm) cc_final: 0.8637 (mmm) REVERT: D 129 ASP cc_start: 0.7319 (p0) cc_final: 0.7090 (p0) REVERT: E 185 LEU cc_start: 0.8118 (tp) cc_final: 0.7899 (mt) REVERT: F 62 ASP cc_start: 0.8566 (p0) cc_final: 0.8036 (p0) REVERT: F 82 ASP cc_start: 0.8482 (p0) cc_final: 0.8265 (p0) REVERT: F 159 THR cc_start: 0.8550 (p) cc_final: 0.8204 (p) REVERT: F 196 PHE cc_start: 0.7544 (m-80) cc_final: 0.6994 (m-10) REVERT: G 1 MET cc_start: 0.7122 (ttt) cc_final: 0.5623 (ttm) REVERT: G 44 GLN cc_start: 0.8367 (tt0) cc_final: 0.8095 (tt0) REVERT: G 49 GLN cc_start: 0.8771 (mm110) cc_final: 0.8530 (mm110) REVERT: G 92 ASN cc_start: 0.8784 (m-40) cc_final: 0.8554 (m-40) REVERT: G 96 PHE cc_start: 0.7090 (m-80) cc_final: 0.6864 (m-10) REVERT: G 198 ASN cc_start: 0.6530 (m-40) cc_final: 0.5715 (m-40) REVERT: H 131 PHE cc_start: 0.8685 (m-80) cc_final: 0.8296 (m-80) REVERT: H 174 LEU cc_start: 0.9352 (tp) cc_final: 0.9078 (tt) REVERT: I 183 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7280 (mt-10) REVERT: I 196 PHE cc_start: 0.8626 (m-80) cc_final: 0.8397 (m-80) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3169 time to fit residues: 173.5479 Evaluate side-chains 283 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 6.9990 chunk 128 optimal weight: 0.0020 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 92 ASN A 198 ASN D 44 GLN D 94 ASN D 105 ASN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 101 ASN G 152 ASN H 25 GLN H 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN I 41 ASN I 49 GLN I 94 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12537 Z= 0.200 Angle : 0.629 11.666 17001 Z= 0.329 Chirality : 0.041 0.157 2143 Planarity : 0.004 0.036 2174 Dihedral : 4.389 19.773 1773 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1709 helix: 0.91 (0.19), residues: 747 sheet: -0.51 (0.32), residues: 221 loop : -1.62 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE E 196 TYR 0.016 0.002 TYR C 133 ARG 0.004 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 341 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8351 (mm110) REVERT: A 41 ASN cc_start: 0.8384 (m-40) cc_final: 0.7921 (p0) REVERT: A 93 MET cc_start: 0.6618 (mtt) cc_final: 0.6366 (mtt) REVERT: A 137 LYS cc_start: 0.9283 (tptt) cc_final: 0.8951 (mppt) REVERT: A 173 ASN cc_start: 0.8646 (t0) cc_final: 0.8205 (p0) REVERT: B 33 MET cc_start: 0.8585 (mmm) cc_final: 0.8265 (mmm) REVERT: B 94 ASN cc_start: 0.8282 (t0) cc_final: 0.7331 (t0) REVERT: B 96 PHE cc_start: 0.7650 (m-80) cc_final: 0.6653 (m-10) REVERT: B 133 TYR cc_start: 0.7930 (t80) cc_final: 0.7594 (t80) REVERT: C 96 PHE cc_start: 0.5252 (m-10) cc_final: 0.5010 (m-10) REVERT: C 129 ASP cc_start: 0.8981 (p0) cc_final: 0.8744 (p0) REVERT: C 131 PHE cc_start: 0.6871 (m-80) cc_final: 0.6568 (m-80) REVERT: C 151 GLU cc_start: 0.8491 (mp0) cc_final: 0.8137 (pm20) REVERT: D 13 MET cc_start: 0.8803 (mmm) cc_final: 0.8447 (mmm) REVERT: D 129 ASP cc_start: 0.7148 (p0) cc_final: 0.6752 (p0) REVERT: D 174 LEU cc_start: 0.8957 (mp) cc_final: 0.8660 (mp) REVERT: E 25 GLN cc_start: 0.7775 (mt0) cc_final: 0.7380 (mt0) REVERT: E 83 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8451 (tp30) REVERT: F 44 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F 62 ASP cc_start: 0.8546 (p0) cc_final: 0.8016 (p0) REVERT: G 38 GLN cc_start: 0.8729 (tp40) cc_final: 0.8476 (tp-100) REVERT: G 49 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8580 (mm110) REVERT: G 92 ASN cc_start: 0.8748 (m-40) cc_final: 0.8544 (m-40) REVERT: H 98 PHE cc_start: 0.7506 (p90) cc_final: 0.7194 (p90) REVERT: H 174 LEU cc_start: 0.9379 (tp) cc_final: 0.9177 (tt) REVERT: I 13 MET cc_start: 0.8192 (mmm) cc_final: 0.7850 (mtt) REVERT: I 92 ASN cc_start: 0.7690 (p0) cc_final: 0.7425 (p0) REVERT: I 183 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7270 (mt-10) REVERT: I 196 PHE cc_start: 0.8446 (m-80) cc_final: 0.8079 (m-10) outliers start: 25 outliers final: 15 residues processed: 352 average time/residue: 0.2901 time to fit residues: 139.1010 Evaluate side-chains 295 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 280 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 120 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 105 ASN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 44 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN F 38 GLN F 41 ASN G 41 ASN G 56 ASN G 198 ASN H 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12537 Z= 0.287 Angle : 0.673 11.506 17001 Z= 0.358 Chirality : 0.042 0.212 2143 Planarity : 0.004 0.036 2174 Dihedral : 4.940 21.599 1773 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.76 % Allowed : 20.02 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1709 helix: 0.91 (0.19), residues: 744 sheet: -0.31 (0.33), residues: 221 loop : -1.37 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 196 TYR 0.016 0.002 TYR F 133 ARG 0.004 0.001 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 298 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7829 (tptt) REVERT: A 93 MET cc_start: 0.6687 (mtt) cc_final: 0.6451 (mtt) REVERT: A 137 LYS cc_start: 0.9219 (tptt) cc_final: 0.8957 (mppt) REVERT: A 173 ASN cc_start: 0.8597 (t0) cc_final: 0.8167 (p0) REVERT: B 1 MET cc_start: 0.8987 (tpp) cc_final: 0.8775 (tpp) REVERT: B 83 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 96 PHE cc_start: 0.7752 (m-80) cc_final: 0.7281 (m-10) REVERT: B 133 TYR cc_start: 0.7981 (t80) cc_final: 0.7636 (t80) REVERT: C 78 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7692 (mmmt) REVERT: C 110 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (mp) REVERT: C 129 ASP cc_start: 0.9000 (p0) cc_final: 0.8739 (p0) REVERT: D 13 MET cc_start: 0.8769 (mmm) cc_final: 0.8544 (mmm) REVERT: D 68 LYS cc_start: 0.8536 (mttt) cc_final: 0.8187 (mttt) REVERT: E 68 LYS cc_start: 0.9039 (mttp) cc_final: 0.8754 (mmtp) REVERT: F 44 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7647 (tm-30) REVERT: F 62 ASP cc_start: 0.8463 (p0) cc_final: 0.7952 (p0) REVERT: G 38 GLN cc_start: 0.8775 (tp40) cc_final: 0.8503 (tp-100) REVERT: G 49 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8686 (mm110) REVERT: G 52 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8415 (mmm160) REVERT: G 92 ASN cc_start: 0.8785 (m-40) cc_final: 0.8573 (m-40) REVERT: G 130 MET cc_start: 0.7842 (mtp) cc_final: 0.7641 (mtm) REVERT: H 83 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7799 (tp30) REVERT: H 98 PHE cc_start: 0.7418 (p90) cc_final: 0.7119 (p90) REVERT: I 92 ASN cc_start: 0.7793 (p0) cc_final: 0.7432 (p0) REVERT: I 96 PHE cc_start: 0.8297 (m-80) cc_final: 0.8047 (m-80) REVERT: I 183 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7300 (mt-10) REVERT: I 196 PHE cc_start: 0.8483 (m-80) cc_final: 0.8205 (m-10) outliers start: 36 outliers final: 22 residues processed: 319 average time/residue: 0.2737 time to fit residues: 119.2677 Evaluate side-chains 282 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 259 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 94 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN F 38 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12537 Z= 0.270 Angle : 0.664 12.394 17001 Z= 0.350 Chirality : 0.042 0.159 2143 Planarity : 0.004 0.037 2174 Dihedral : 5.018 23.465 1773 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.45 % Allowed : 22.85 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1709 helix: 0.85 (0.19), residues: 749 sheet: -0.18 (0.34), residues: 216 loop : -1.26 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE C 131 TYR 0.016 0.002 TYR C 133 ARG 0.007 0.001 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7751 (tptt) REVERT: A 137 LYS cc_start: 0.9227 (tptt) cc_final: 0.8955 (mppt) REVERT: B 1 MET cc_start: 0.8959 (tpp) cc_final: 0.8482 (tpp) REVERT: B 33 MET cc_start: 0.8599 (mmm) cc_final: 0.8342 (mmm) REVERT: B 83 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8179 (mp0) REVERT: B 96 PHE cc_start: 0.7814 (m-80) cc_final: 0.7361 (m-10) REVERT: B 133 TYR cc_start: 0.8024 (t80) cc_final: 0.7687 (t80) REVERT: B 165 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7897 (ptmm) REVERT: C 78 LYS cc_start: 0.8373 (mmmm) cc_final: 0.7586 (tptp) REVERT: C 129 ASP cc_start: 0.9041 (p0) cc_final: 0.8818 (p0) REVERT: D 13 MET cc_start: 0.8766 (mmm) cc_final: 0.8466 (mmm) REVERT: E 62 ASP cc_start: 0.8573 (p0) cc_final: 0.8325 (p0) REVERT: F 44 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7678 (tm-30) REVERT: F 62 ASP cc_start: 0.8458 (p0) cc_final: 0.7966 (p0) REVERT: G 38 GLN cc_start: 0.8818 (tp40) cc_final: 0.8552 (tp-100) REVERT: G 47 LEU cc_start: 0.8732 (tp) cc_final: 0.8524 (tp) REVERT: G 49 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8668 (mm110) REVERT: G 52 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8637 (mmm160) REVERT: G 92 ASN cc_start: 0.8811 (m-40) cc_final: 0.8598 (m-40) REVERT: H 83 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7816 (tp30) REVERT: H 98 PHE cc_start: 0.7403 (p90) cc_final: 0.7132 (p90) REVERT: H 129 ASP cc_start: 0.7623 (p0) cc_final: 0.7331 (p0) REVERT: H 164 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8762 (mm) REVERT: I 83 GLU cc_start: 0.8344 (pt0) cc_final: 0.7798 (pt0) REVERT: I 96 PHE cc_start: 0.8208 (m-80) cc_final: 0.7871 (m-80) REVERT: I 183 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7270 (mt-10) REVERT: I 196 PHE cc_start: 0.8453 (m-80) cc_final: 0.8197 (m-10) outliers start: 45 outliers final: 27 residues processed: 311 average time/residue: 0.2683 time to fit residues: 115.2112 Evaluate side-chains 284 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 129 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 25 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12537 Z= 0.226 Angle : 0.644 8.373 17001 Z= 0.336 Chirality : 0.041 0.190 2143 Planarity : 0.004 0.036 2174 Dihedral : 4.920 24.158 1773 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.76 % Allowed : 24.77 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1709 helix: 1.06 (0.19), residues: 744 sheet: -0.12 (0.34), residues: 212 loop : -1.25 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE E 196 TYR 0.011 0.002 TYR F 133 ARG 0.005 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 279 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LYS cc_start: 0.9209 (tptt) cc_final: 0.8946 (mppt) REVERT: B 1 MET cc_start: 0.8948 (tpp) cc_final: 0.8579 (tpp) REVERT: B 33 MET cc_start: 0.8609 (mmm) cc_final: 0.8348 (mmm) REVERT: B 133 TYR cc_start: 0.7960 (t80) cc_final: 0.7630 (t80) REVERT: C 33 MET cc_start: 0.8650 (tmm) cc_final: 0.8236 (tmm) REVERT: C 78 LYS cc_start: 0.8358 (mmmm) cc_final: 0.7379 (tptp) REVERT: C 96 PHE cc_start: 0.5244 (m-10) cc_final: 0.5009 (m-10) REVERT: C 129 ASP cc_start: 0.9079 (p0) cc_final: 0.8862 (p0) REVERT: C 196 PHE cc_start: 0.8724 (m-80) cc_final: 0.8164 (m-80) REVERT: D 13 MET cc_start: 0.8701 (mmm) cc_final: 0.8426 (mmm) REVERT: E 62 ASP cc_start: 0.8603 (p0) cc_final: 0.8334 (p0) REVERT: F 44 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 62 ASP cc_start: 0.8485 (p0) cc_final: 0.7993 (p0) REVERT: G 38 GLN cc_start: 0.8809 (tp40) cc_final: 0.8539 (tp-100) REVERT: G 47 LEU cc_start: 0.8745 (tp) cc_final: 0.8542 (tp) REVERT: G 49 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8677 (mm110) REVERT: G 92 ASN cc_start: 0.8793 (m-40) cc_final: 0.8535 (m-40) REVERT: H 83 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7824 (tp30) REVERT: H 98 PHE cc_start: 0.7421 (p90) cc_final: 0.7101 (p90) REVERT: H 183 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8407 (pt0) REVERT: I 96 PHE cc_start: 0.8125 (m-80) cc_final: 0.7852 (m-80) REVERT: I 183 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7316 (mt-10) REVERT: I 196 PHE cc_start: 0.8449 (m-80) cc_final: 0.8186 (m-10) outliers start: 49 outliers final: 36 residues processed: 313 average time/residue: 0.2813 time to fit residues: 120.7919 Evaluate side-chains 292 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 129 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12537 Z= 0.201 Angle : 0.641 9.439 17001 Z= 0.334 Chirality : 0.041 0.146 2143 Planarity : 0.003 0.039 2174 Dihedral : 4.813 24.000 1773 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.22 % Allowed : 24.77 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1709 helix: 1.18 (0.19), residues: 745 sheet: 0.06 (0.34), residues: 210 loop : -1.19 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE E 196 TYR 0.012 0.001 TYR G 51 ARG 0.007 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8065 (tmtt) cc_final: 0.7834 (tptt) REVERT: A 82 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8527 (p0) REVERT: A 137 LYS cc_start: 0.9184 (tptt) cc_final: 0.8933 (mppt) REVERT: A 173 ASN cc_start: 0.8601 (t0) cc_final: 0.8143 (p0) REVERT: B 1 MET cc_start: 0.8926 (tpp) cc_final: 0.8428 (tpp) REVERT: B 33 MET cc_start: 0.8643 (mmm) cc_final: 0.8381 (mmm) REVERT: B 96 PHE cc_start: 0.7922 (m-10) cc_final: 0.7565 (m-10) REVERT: C 33 MET cc_start: 0.8715 (tmm) cc_final: 0.8336 (tmm) REVERT: C 129 ASP cc_start: 0.9085 (p0) cc_final: 0.8850 (p0) REVERT: C 196 PHE cc_start: 0.8621 (m-80) cc_final: 0.8225 (m-80) REVERT: D 13 MET cc_start: 0.8671 (mmm) cc_final: 0.8449 (mmm) REVERT: E 62 ASP cc_start: 0.8563 (p0) cc_final: 0.8276 (p0) REVERT: F 44 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7656 (tm-30) REVERT: F 62 ASP cc_start: 0.8472 (p0) cc_final: 0.7974 (p0) REVERT: F 100 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8609 (ttp80) REVERT: F 112 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8623 (m) REVERT: G 38 GLN cc_start: 0.8792 (tp40) cc_final: 0.8545 (tp-100) REVERT: G 49 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8628 (mm110) REVERT: G 92 ASN cc_start: 0.8786 (m-40) cc_final: 0.8506 (m-40) REVERT: G 96 PHE cc_start: 0.6978 (m-80) cc_final: 0.6672 (m-10) REVERT: H 98 PHE cc_start: 0.7436 (p90) cc_final: 0.7101 (p90) REVERT: H 129 ASP cc_start: 0.7422 (p0) cc_final: 0.6246 (p0) REVERT: H 174 LEU cc_start: 0.9350 (tp) cc_final: 0.8703 (mp) REVERT: I 75 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7609 (p) REVERT: I 96 PHE cc_start: 0.8043 (m-80) cc_final: 0.7831 (m-80) REVERT: I 183 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7341 (mt-10) REVERT: I 196 PHE cc_start: 0.8442 (m-80) cc_final: 0.8173 (m-10) outliers start: 55 outliers final: 35 residues processed: 316 average time/residue: 0.2729 time to fit residues: 121.7824 Evaluate side-chains 291 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12537 Z= 0.264 Angle : 0.701 9.281 17001 Z= 0.364 Chirality : 0.042 0.226 2143 Planarity : 0.004 0.041 2174 Dihedral : 5.071 23.957 1773 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.76 % Allowed : 27.15 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1709 helix: 1.03 (0.19), residues: 747 sheet: 0.05 (0.34), residues: 210 loop : -1.24 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.002 PHE E 196 TYR 0.016 0.002 TYR G 51 ARG 0.004 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7839 (tptt) REVERT: A 82 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8569 (p0) REVERT: A 137 LYS cc_start: 0.9240 (tptt) cc_final: 0.8977 (mppt) REVERT: B 1 MET cc_start: 0.8927 (tpp) cc_final: 0.8502 (tpp) REVERT: B 25 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: B 33 MET cc_start: 0.8584 (mmm) cc_final: 0.8328 (mmm) REVERT: B 96 PHE cc_start: 0.7979 (m-10) cc_final: 0.7671 (m-10) REVERT: C 129 ASP cc_start: 0.9101 (p0) cc_final: 0.8860 (p0) REVERT: C 131 PHE cc_start: 0.6994 (m-80) cc_final: 0.6770 (m-10) REVERT: C 196 PHE cc_start: 0.8657 (m-80) cc_final: 0.8297 (m-80) REVERT: D 13 MET cc_start: 0.8702 (mmm) cc_final: 0.8459 (mmm) REVERT: D 94 ASN cc_start: 0.8986 (m-40) cc_final: 0.8739 (m110) REVERT: E 196 PHE cc_start: 0.7948 (m-10) cc_final: 0.7694 (m-80) REVERT: F 44 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7736 (tm-30) REVERT: F 62 ASP cc_start: 0.8427 (p0) cc_final: 0.7947 (p0) REVERT: F 100 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8588 (ttp80) REVERT: G 38 GLN cc_start: 0.8818 (tp40) cc_final: 0.8563 (tp-100) REVERT: G 47 LEU cc_start: 0.8717 (tp) cc_final: 0.8508 (tp) REVERT: G 49 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8612 (mm110) REVERT: G 96 PHE cc_start: 0.7080 (m-80) cc_final: 0.6748 (m-10) REVERT: H 98 PHE cc_start: 0.7457 (p90) cc_final: 0.7113 (p90) REVERT: I 75 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7714 (p) REVERT: I 96 PHE cc_start: 0.8054 (m-80) cc_final: 0.7821 (m-80) REVERT: I 183 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7373 (mt-10) REVERT: I 196 PHE cc_start: 0.8441 (m-80) cc_final: 0.8175 (m-10) outliers start: 49 outliers final: 37 residues processed: 299 average time/residue: 0.2634 time to fit residues: 109.4412 Evaluate side-chains 288 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 248 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12537 Z= 0.202 Angle : 0.680 10.815 17001 Z= 0.352 Chirality : 0.042 0.217 2143 Planarity : 0.003 0.044 2174 Dihedral : 4.874 24.169 1773 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.60 % Allowed : 28.14 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1709 helix: 1.18 (0.19), residues: 747 sheet: 0.16 (0.35), residues: 210 loop : -1.14 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHE E 196 TYR 0.019 0.002 TYR G 57 ARG 0.006 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 260 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7809 (tptt) REVERT: A 137 LYS cc_start: 0.9200 (tptt) cc_final: 0.8959 (mppt) REVERT: B 1 MET cc_start: 0.8859 (tpp) cc_final: 0.8453 (tpp) REVERT: B 33 MET cc_start: 0.8652 (mmm) cc_final: 0.8397 (mmm) REVERT: B 96 PHE cc_start: 0.7880 (m-10) cc_final: 0.7573 (m-10) REVERT: C 131 PHE cc_start: 0.7002 (m-80) cc_final: 0.6779 (m-10) REVERT: C 196 PHE cc_start: 0.8586 (m-80) cc_final: 0.8295 (m-80) REVERT: D 13 MET cc_start: 0.8691 (mmm) cc_final: 0.8423 (mmm) REVERT: E 62 ASP cc_start: 0.8497 (p0) cc_final: 0.8174 (p0) REVERT: E 196 PHE cc_start: 0.7877 (m-10) cc_final: 0.7610 (m-80) REVERT: F 44 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7694 (tm-30) REVERT: F 62 ASP cc_start: 0.8493 (p0) cc_final: 0.7992 (p0) REVERT: F 100 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8554 (ttp80) REVERT: G 1 MET cc_start: 0.6964 (ttt) cc_final: 0.6352 (tmm) REVERT: G 38 GLN cc_start: 0.8798 (tp40) cc_final: 0.8535 (tp-100) REVERT: G 49 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8381 (mm110) REVERT: G 96 PHE cc_start: 0.6936 (m-80) cc_final: 0.6606 (m-10) REVERT: H 113 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6523 (p0) REVERT: H 129 ASP cc_start: 0.7530 (p0) cc_final: 0.7127 (p0) REVERT: H 174 LEU cc_start: 0.9309 (tp) cc_final: 0.8643 (mp) REVERT: I 183 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7346 (mt-10) REVERT: I 196 PHE cc_start: 0.8465 (m-80) cc_final: 0.8190 (m-10) outliers start: 47 outliers final: 38 residues processed: 294 average time/residue: 0.2561 time to fit residues: 105.2484 Evaluate side-chains 286 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 247 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 0.0030 chunk 46 optimal weight: 0.0970 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 overall best weight: 4.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12537 Z= 0.261 Angle : 0.725 12.251 17001 Z= 0.374 Chirality : 0.042 0.214 2143 Planarity : 0.004 0.048 2174 Dihedral : 5.074 24.943 1773 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.83 % Allowed : 28.22 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1709 helix: 0.99 (0.19), residues: 752 sheet: 0.11 (0.36), residues: 201 loop : -1.21 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 196 TYR 0.017 0.002 TYR G 51 ARG 0.006 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7802 (tptt) REVERT: A 137 LYS cc_start: 0.9252 (tptt) cc_final: 0.8963 (mppt) REVERT: B 1 MET cc_start: 0.8829 (tpp) cc_final: 0.8538 (tpp) REVERT: B 33 MET cc_start: 0.8610 (mmm) cc_final: 0.8347 (mmm) REVERT: B 96 PHE cc_start: 0.7769 (m-10) cc_final: 0.7456 (m-10) REVERT: B 196 PHE cc_start: 0.8514 (m-80) cc_final: 0.8312 (m-10) REVERT: C 196 PHE cc_start: 0.8601 (m-80) cc_final: 0.8318 (m-80) REVERT: D 13 MET cc_start: 0.8718 (mmm) cc_final: 0.8431 (mmm) REVERT: E 62 ASP cc_start: 0.8574 (p0) cc_final: 0.8299 (p0) REVERT: E 196 PHE cc_start: 0.8042 (m-10) cc_final: 0.7658 (m-80) REVERT: F 44 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7877 (tm-30) REVERT: F 62 ASP cc_start: 0.8468 (p0) cc_final: 0.7970 (p0) REVERT: F 93 MET cc_start: 0.8252 (mmm) cc_final: 0.8012 (tpt) REVERT: G 38 GLN cc_start: 0.8811 (tp40) cc_final: 0.8545 (tp-100) REVERT: G 49 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8438 (mm110) REVERT: G 96 PHE cc_start: 0.7076 (m-80) cc_final: 0.6746 (m-10) REVERT: H 98 PHE cc_start: 0.7498 (p90) cc_final: 0.7159 (p90) REVERT: H 129 ASP cc_start: 0.7550 (p0) cc_final: 0.7214 (p0) REVERT: H 183 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8613 (pt0) REVERT: I 183 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7315 (mt-10) REVERT: I 196 PHE cc_start: 0.8473 (m-80) cc_final: 0.8231 (m-10) outliers start: 50 outliers final: 45 residues processed: 289 average time/residue: 0.2508 time to fit residues: 102.2681 Evaluate side-chains 293 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 173 ASN Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN G 152 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12537 Z= 0.245 Angle : 0.730 13.700 17001 Z= 0.374 Chirality : 0.042 0.212 2143 Planarity : 0.004 0.049 2174 Dihedral : 5.089 25.483 1773 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.60 % Allowed : 29.29 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1709 helix: 1.05 (0.19), residues: 750 sheet: 0.13 (0.36), residues: 201 loop : -1.23 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE E 196 TYR 0.018 0.002 TYR G 51 ARG 0.008 0.001 ARG I 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7794 (tptt) REVERT: A 137 LYS cc_start: 0.9227 (tptt) cc_final: 0.8950 (mppt) REVERT: A 172 LYS cc_start: 0.8961 (ptmm) cc_final: 0.8515 (pptt) REVERT: B 1 MET cc_start: 0.8786 (tpp) cc_final: 0.8529 (tpp) REVERT: B 33 MET cc_start: 0.8650 (mmm) cc_final: 0.8405 (mmm) REVERT: B 96 PHE cc_start: 0.7768 (m-10) cc_final: 0.7475 (m-10) REVERT: B 131 PHE cc_start: 0.7125 (m-10) cc_final: 0.6609 (m-10) REVERT: B 165 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7862 (ptmm) REVERT: C 131 PHE cc_start: 0.6931 (m-10) cc_final: 0.6427 (m-10) REVERT: D 13 MET cc_start: 0.8714 (mmm) cc_final: 0.8419 (mmm) REVERT: E 62 ASP cc_start: 0.8536 (p0) cc_final: 0.8248 (p0) REVERT: E 196 PHE cc_start: 0.7992 (m-10) cc_final: 0.7602 (m-80) REVERT: F 44 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7861 (tm-30) REVERT: F 62 ASP cc_start: 0.8497 (p0) cc_final: 0.7998 (p0) REVERT: F 93 MET cc_start: 0.8241 (mmm) cc_final: 0.8006 (tpt) REVERT: F 100 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8700 (ttp80) REVERT: G 38 GLN cc_start: 0.8814 (tp40) cc_final: 0.8563 (tp-100) REVERT: G 49 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8448 (mm110) REVERT: G 96 PHE cc_start: 0.6982 (m-80) cc_final: 0.6663 (m-10) REVERT: H 98 PHE cc_start: 0.7501 (p90) cc_final: 0.7185 (p90) REVERT: H 129 ASP cc_start: 0.7566 (p0) cc_final: 0.7279 (p0) REVERT: H 174 LEU cc_start: 0.9358 (tp) cc_final: 0.8702 (mp) REVERT: H 183 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8581 (pt0) REVERT: I 183 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7313 (mt-10) REVERT: I 196 PHE cc_start: 0.8469 (m-80) cc_final: 0.8223 (m-10) outliers start: 47 outliers final: 42 residues processed: 282 average time/residue: 0.2656 time to fit residues: 104.7798 Evaluate side-chains 289 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 129 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 138 optimal weight: 0.1980 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 94 ASN D 101 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044287 restraints weight = 81919.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.045477 restraints weight = 48392.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046283 restraints weight = 32410.104| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12537 Z= 0.193 Angle : 0.707 15.558 17001 Z= 0.359 Chirality : 0.042 0.213 2143 Planarity : 0.003 0.054 2174 Dihedral : 4.748 25.706 1773 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.68 % Allowed : 30.21 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1709 helix: 1.32 (0.19), residues: 742 sheet: 0.32 (0.37), residues: 198 loop : -1.15 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE E 196 TYR 0.017 0.001 TYR G 51 ARG 0.009 0.001 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.09 seconds wall clock time: 55 minutes 7.18 seconds (3307.18 seconds total)