Starting phenix.real_space_refine on Mon Aug 5 03:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/08_2024/8uhf_42279.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/08_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_42279/08_2024/8uhf_42279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/08_2024/8uhf_42279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/08_2024/8uhf_42279.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/08_2024/8uhf_42279.cif" } 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-5409/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: 7.24, per 1000 atoms: 0.58 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: 4.94 Conformation dependent library (CDL) restraints added in 2.4 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: 1.33 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: 3.24 Time building geometry restraints manager: 5.39 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 3.040 nonbonded pdb=" OG SER A 39 " pdb=" O GLU A 83 " model vdw 2.202 3.040 nonbonded pdb=" OG SER F 80 " pdb=" OD1 ASP F 82 " model vdw 2.218 3.040 nonbonded pdb=" O ASP H 149 " pdb=" OG SER H 153 " model vdw 2.240 3.040 nonbonded pdb=" O GLY E 128 " pdb=" NZ LYS E 165 " model vdw 2.247 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.700 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.270 Find NCS groups from input model: 0.690 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- 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 : 1.425 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: 0.3067 time to fit residues: 168.4322 Evaluate side-chains 283 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 133 optimal weight: 0.0470 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 overall best weight: 2.3884 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN C 44 GLN C 117 GLN D 44 GLN D 94 ASN D 105 ASN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 101 ASN 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 94 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2890 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= 0.205 Angle : 0.652 11.763 17001 Z= 0.342 Chirality : 0.042 0.160 2143 Planarity : 0.004 0.035 2174 Dihedral : 4.417 19.742 1773 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.23 % Allowed : 15.87 % Favored : 82.90 % 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: -0.62 (0.20), residues: 1709 helix: 0.81 (0.19), residues: 753 sheet: -0.53 (0.32), residues: 222 loop : -1.67 (0.21), residues: 734 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 0.005 0.001 ARG F 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 357 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 341 time to evaluate : 1.491 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 93 MET cc_start: 0.6576 (mtt) cc_final: 0.6323 (mtt) REVERT: A 137 LYS cc_start: 0.9290 (tptt) cc_final: 0.8944 (mppt) REVERT: A 173 ASN cc_start: 0.8643 (t0) cc_final: 0.8187 (p0) REVERT: B 33 MET cc_start: 0.8621 (mmm) cc_final: 0.8282 (mmm) REVERT: B 51 TYR cc_start: 0.7098 (m-80) cc_final: 0.6893 (m-80) REVERT: B 94 ASN cc_start: 0.8293 (t0) cc_final: 0.7342 (t0) REVERT: B 96 PHE cc_start: 0.7672 (m-80) cc_final: 0.6690 (m-10) REVERT: B 133 TYR cc_start: 0.7914 (t80) cc_final: 0.7533 (t80) REVERT: C 33 MET cc_start: 0.8712 (tmm) cc_final: 0.8412 (tmm) REVERT: C 78 LYS cc_start: 0.8449 (mmmm) cc_final: 0.7837 (mmmt) REVERT: C 129 ASP cc_start: 0.8914 (p0) cc_final: 0.8678 (p0) REVERT: C 131 PHE cc_start: 0.6856 (m-80) cc_final: 0.6600 (m-80) REVERT: C 192 PHE cc_start: 0.6531 (m-80) cc_final: 0.6295 (m-10) REVERT: D 13 MET cc_start: 0.8806 (mmm) cc_final: 0.8493 (mmm) REVERT: D 129 ASP cc_start: 0.7111 (p0) cc_final: 0.6737 (p0) REVERT: D 174 LEU cc_start: 0.8958 (mp) cc_final: 0.8662 (mp) REVERT: E 25 GLN cc_start: 0.7761 (mt0) cc_final: 0.7366 (mt0) REVERT: E 83 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8390 (tp30) REVERT: F 44 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7706 (tm-30) REVERT: F 62 ASP cc_start: 0.8544 (p0) cc_final: 0.8035 (p0) REVERT: G 38 GLN cc_start: 0.8714 (tp40) cc_final: 0.8464 (tp-100) REVERT: G 49 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8590 (mm110) REVERT: H 98 PHE cc_start: 0.7509 (p90) cc_final: 0.7176 (p90) REVERT: I 183 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7183 (mt-10) REVERT: I 196 PHE cc_start: 0.8403 (m-80) cc_final: 0.7952 (m-10) outliers start: 16 outliers final: 8 residues processed: 347 average time/residue: 0.2917 time to fit residues: 136.8304 Evaluate side-chains 280 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 272 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 119 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN G 101 ASN G 152 ASN G 198 ASN H 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12537 Z= 0.211 Angle : 0.653 12.324 17001 Z= 0.342 Chirality : 0.042 0.213 2143 Planarity : 0.004 0.038 2174 Dihedral : 4.570 20.003 1773 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.92 % Allowed : 19.71 % Favored : 78.37 % 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: -0.19 (0.20), residues: 1709 helix: 1.09 (0.19), residues: 756 sheet: -0.20 (0.34), residues: 212 loop : -1.38 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE E 196 TYR 0.015 0.001 TYR F 133 ARG 0.010 0.001 ARG C 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 328 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 303 time to evaluate : 1.555 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: A 41 ASN cc_start: 0.8512 (m-40) cc_final: 0.8295 (p0) REVERT: A 93 MET cc_start: 0.6522 (mtt) cc_final: 0.6290 (mtt) REVERT: A 137 LYS cc_start: 0.9139 (tptt) cc_final: 0.8905 (mppt) REVERT: A 173 ASN cc_start: 0.8545 (t0) cc_final: 0.8122 (p0) REVERT: B 1 MET cc_start: 0.8887 (tpp) cc_final: 0.8493 (tpp) REVERT: B 94 ASN cc_start: 0.8276 (t0) cc_final: 0.7262 (t0) REVERT: B 96 PHE cc_start: 0.7639 (m-80) cc_final: 0.6550 (m-10) REVERT: C 129 ASP cc_start: 0.8912 (p0) cc_final: 0.8684 (p0) REVERT: D 13 MET cc_start: 0.8781 (mmm) cc_final: 0.8473 (mmm) REVERT: D 129 ASP cc_start: 0.7187 (p0) cc_final: 0.6878 (p0) REVERT: E 68 LYS cc_start: 0.9098 (mttp) cc_final: 0.8832 (mmtp) REVERT: E 83 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8479 (tp30) REVERT: E 174 LEU cc_start: 0.8180 (tp) cc_final: 0.7974 (tt) REVERT: F 33 MET cc_start: 0.8275 (tpp) cc_final: 0.8057 (tpp) REVERT: F 44 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 62 ASP cc_start: 0.8522 (p0) cc_final: 0.8033 (p0) REVERT: G 38 GLN cc_start: 0.8729 (tp40) cc_final: 0.8427 (tp-100) REVERT: G 49 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8609 (mm110) REVERT: H 83 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7800 (tp30) REVERT: H 98 PHE cc_start: 0.7453 (p90) cc_final: 0.7051 (p90) REVERT: H 100 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7854 (ttp-110) REVERT: H 174 LEU cc_start: 0.9240 (tt) cc_final: 0.8438 (mp) REVERT: I 13 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: I 183 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7309 (mt-10) REVERT: I 196 PHE cc_start: 0.8443 (m-80) cc_final: 0.7966 (m-10) outliers start: 25 outliers final: 11 residues processed: 313 average time/residue: 0.2680 time to fit residues: 116.9644 Evaluate side-chains 276 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 175 ASP Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 92 ASN 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: 9.9990 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 0.0770 chunk 44 optimal weight: 7.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 119 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12537 Z= 0.171 Angle : 0.622 11.645 17001 Z= 0.324 Chirality : 0.041 0.142 2143 Planarity : 0.003 0.035 2174 Dihedral : 4.423 20.428 1773 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.84 % Allowed : 21.09 % Favored : 77.07 % 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: 0.05 (0.20), residues: 1709 helix: 1.27 (0.19), residues: 757 sheet: 0.03 (0.35), residues: 219 loop : -1.29 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE C 192 TYR 0.016 0.002 TYR E 133 ARG 0.007 0.001 ARG A 100 *********************** 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 322 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 298 time to evaluate : 2.001 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 41 ASN cc_start: 0.8573 (m-40) cc_final: 0.8347 (m-40) REVERT: A 68 LYS cc_start: 0.8027 (tmtt) cc_final: 0.7777 (tptt) REVERT: A 83 GLU cc_start: 0.7734 (pt0) cc_final: 0.7458 (pt0) REVERT: A 137 LYS cc_start: 0.9078 (tptt) cc_final: 0.8853 (mppt) REVERT: A 173 ASN cc_start: 0.8556 (t0) cc_final: 0.8129 (p0) REVERT: B 1 MET cc_start: 0.8881 (tpp) cc_final: 0.8647 (tpp) REVERT: B 94 ASN cc_start: 0.8295 (t0) cc_final: 0.7380 (t0) REVERT: B 96 PHE cc_start: 0.7733 (m-80) cc_final: 0.6645 (m-10) REVERT: C 129 ASP cc_start: 0.8939 (p0) cc_final: 0.8669 (p0) REVERT: D 13 MET cc_start: 0.8694 (mmm) cc_final: 0.8493 (mmm) REVERT: F 44 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7662 (tm-30) REVERT: F 62 ASP cc_start: 0.8542 (p0) cc_final: 0.8047 (p0) REVERT: F 83 GLU cc_start: 0.8094 (pp20) cc_final: 0.7891 (tm-30) REVERT: G 38 GLN cc_start: 0.8702 (tp40) cc_final: 0.8367 (tp-100) REVERT: G 49 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8585 (mm110) REVERT: H 83 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7780 (tp30) REVERT: H 174 LEU cc_start: 0.8915 (tt) cc_final: 0.8287 (mp) REVERT: I 183 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7300 (mt-10) REVERT: I 196 PHE cc_start: 0.8413 (m-80) cc_final: 0.8006 (m-10) outliers start: 24 outliers final: 7 residues processed: 312 average time/residue: 0.2860 time to fit residues: 123.4257 Evaluate side-chains 267 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 260 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 25 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 94 ASN D 117 GLN E 44 GLN E 105 ASN G 56 ASN G 101 ASN G 173 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12537 Z= 0.306 Angle : 0.737 9.858 17001 Z= 0.388 Chirality : 0.043 0.209 2143 Planarity : 0.004 0.044 2174 Dihedral : 5.056 22.113 1773 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.38 % Allowed : 22.09 % Favored : 75.54 % 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: -0.22 (0.20), residues: 1709 helix: 0.89 (0.19), residues: 749 sheet: -0.01 (0.35), residues: 218 loop : -1.25 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 196 TYR 0.012 0.002 TYR G 51 ARG 0.008 0.001 ARG H 100 *********************** 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 307 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 1.615 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 33 MET cc_start: 0.8254 (mtm) cc_final: 0.8027 (mtm) REVERT: A 68 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7769 (tptt) REVERT: A 83 GLU cc_start: 0.7956 (pt0) cc_final: 0.7675 (pt0) REVERT: A 137 LYS cc_start: 0.9194 (tptt) cc_final: 0.8877 (mppt) REVERT: A 173 ASN cc_start: 0.8527 (t0) cc_final: 0.8145 (p0) REVERT: B 1 MET cc_start: 0.8932 (tpp) cc_final: 0.8714 (tpp) REVERT: B 83 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8014 (mp0) REVERT: B 96 PHE cc_start: 0.7830 (m-80) cc_final: 0.7288 (m-10) REVERT: C 33 MET cc_start: 0.8680 (tmm) cc_final: 0.8324 (tmm) REVERT: C 129 ASP cc_start: 0.9003 (p0) cc_final: 0.8744 (p0) REVERT: C 151 GLU cc_start: 0.8167 (mp0) cc_final: 0.7936 (mp0) REVERT: D 13 MET cc_start: 0.8755 (mmm) cc_final: 0.8500 (mmm) REVERT: E 35 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8426 (ttmm) REVERT: F 44 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7800 (tm-30) REVERT: F 62 ASP cc_start: 0.8453 (p0) cc_final: 0.7937 (p0) REVERT: G 38 GLN cc_start: 0.8806 (tp40) cc_final: 0.8561 (tp-100) REVERT: G 49 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8573 (mm110) REVERT: H 83 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7933 (tp30) REVERT: H 98 PHE cc_start: 0.7630 (p90) cc_final: 0.7271 (p90) REVERT: H 100 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7967 (ptp-110) REVERT: H 129 ASP cc_start: 0.7386 (p0) cc_final: 0.6937 (p0) REVERT: H 130 MET cc_start: 0.6679 (mmm) cc_final: 0.6307 (mmm) REVERT: I 33 MET cc_start: 0.8968 (tmm) cc_final: 0.8747 (tmm) REVERT: I 78 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8373 (ptpt) REVERT: I 93 MET cc_start: 0.7951 (mmt) cc_final: 0.7713 (mmt) REVERT: I 183 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7306 (mt-10) REVERT: I 196 PHE cc_start: 0.8483 (m-80) cc_final: 0.8067 (m-10) outliers start: 31 outliers final: 19 residues processed: 301 average time/residue: 0.2686 time to fit residues: 111.5507 Evaluate side-chains 271 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 152 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 108 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.0020 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 0.0060 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 overall best weight: 1.9408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 49 GLN D 94 ASN D 117 GLN E 44 GLN G 173 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12537 Z= 0.200 Angle : 0.681 9.501 17001 Z= 0.355 Chirality : 0.042 0.196 2143 Planarity : 0.004 0.046 2174 Dihedral : 4.766 22.928 1773 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.22 % Allowed : 23.93 % Favored : 73.85 % 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 (0.20), residues: 1709 helix: 1.11 (0.19), residues: 749 sheet: 0.15 (0.36), residues: 207 loop : -1.22 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE E 196 TYR 0.011 0.001 TYR G 57 ARG 0.011 0.001 ARG D 100 *********************** 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 303 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 274 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7796 (tptt) REVERT: A 83 GLU cc_start: 0.7942 (pt0) cc_final: 0.7479 (pt0) REVERT: A 129 ASP cc_start: 0.8535 (m-30) cc_final: 0.8009 (m-30) REVERT: A 137 LYS cc_start: 0.9141 (tptt) cc_final: 0.8895 (mppt) REVERT: A 173 ASN cc_start: 0.8501 (t0) cc_final: 0.8118 (p0) REVERT: B 1 MET cc_start: 0.8765 (tpp) cc_final: 0.8473 (tpp) REVERT: B 83 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8021 (mp0) REVERT: B 94 ASN cc_start: 0.8357 (t0) cc_final: 0.7861 (t0) REVERT: B 131 PHE cc_start: 0.6909 (m-10) cc_final: 0.6637 (m-10) REVERT: B 165 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7892 (pttp) REVERT: C 33 MET cc_start: 0.8735 (tmm) cc_final: 0.8400 (tmm) REVERT: C 129 ASP cc_start: 0.8983 (p0) cc_final: 0.8732 (p0) REVERT: C 131 PHE cc_start: 0.7081 (m-80) cc_final: 0.6044 (m-80) REVERT: C 196 PHE cc_start: 0.8607 (m-10) cc_final: 0.8279 (m-80) REVERT: D 13 MET cc_start: 0.8658 (mmm) cc_final: 0.8386 (mmm) REVERT: E 68 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8561 (mptt) REVERT: E 187 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7839 (pttm) REVERT: E 196 PHE cc_start: 0.7871 (m-10) cc_final: 0.7541 (m-80) REVERT: F 44 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 62 ASP cc_start: 0.8480 (p0) cc_final: 0.7974 (p0) REVERT: G 38 GLN cc_start: 0.8766 (tp40) cc_final: 0.8452 (tp-100) REVERT: G 49 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8507 (mm110) REVERT: H 38 GLN cc_start: 0.8628 (mt0) cc_final: 0.8361 (mt0) REVERT: H 83 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7887 (tp30) REVERT: H 98 PHE cc_start: 0.7456 (p90) cc_final: 0.7138 (p90) REVERT: H 100 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.7855 (ptp-110) REVERT: I 183 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7330 (mt-10) REVERT: I 196 PHE cc_start: 0.8442 (m-80) cc_final: 0.8014 (m-10) outliers start: 29 outliers final: 13 residues processed: 295 average time/residue: 0.2562 time to fit residues: 105.8869 Evaluate side-chains 262 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 73 LEU 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: 9.9990 chunk 18 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN E 44 GLN G 119 GLN G 198 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12537 Z= 0.228 Angle : 0.717 16.053 17001 Z= 0.376 Chirality : 0.043 0.243 2143 Planarity : 0.004 0.048 2174 Dihedral : 4.820 22.970 1773 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.30 % Allowed : 24.62 % Favored : 73.08 % 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: 0.05 (0.20), residues: 1709 helix: 1.17 (0.19), residues: 747 sheet: 0.23 (0.36), residues: 205 loop : -1.19 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHE E 196 TYR 0.012 0.001 TYR G 51 ARG 0.010 0.001 ARG D 100 *********************** 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 286 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 256 time to evaluate : 1.299 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 129 ASP cc_start: 0.8564 (m-30) cc_final: 0.8170 (m-30) REVERT: A 137 LYS cc_start: 0.9140 (tptt) cc_final: 0.8926 (mppt) REVERT: A 173 ASN cc_start: 0.8433 (t0) cc_final: 0.8082 (p0) REVERT: B 83 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 96 PHE cc_start: 0.7865 (m-80) cc_final: 0.7504 (m-80) REVERT: C 33 MET cc_start: 0.8751 (tmm) cc_final: 0.8421 (tmm) REVERT: C 131 PHE cc_start: 0.7043 (m-80) cc_final: 0.5993 (m-80) REVERT: C 196 PHE cc_start: 0.8607 (m-10) cc_final: 0.8248 (m-80) REVERT: D 13 MET cc_start: 0.8687 (mmm) cc_final: 0.8469 (mmm) REVERT: E 93 MET cc_start: 0.6837 (mtt) cc_final: 0.6615 (mtt) REVERT: E 196 PHE cc_start: 0.8020 (m-10) cc_final: 0.7664 (m-80) REVERT: F 44 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7794 (tm-30) REVERT: F 62 ASP cc_start: 0.8477 (p0) cc_final: 0.7969 (p0) REVERT: G 38 GLN cc_start: 0.8802 (tp40) cc_final: 0.8500 (tp-100) REVERT: G 49 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8438 (mm110) REVERT: G 96 PHE cc_start: 0.7107 (m-80) cc_final: 0.6856 (m-10) REVERT: G 198 ASN cc_start: 0.5942 (m-40) cc_final: 0.5649 (m-40) REVERT: H 83 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7930 (tp30) REVERT: H 98 PHE cc_start: 0.7418 (p90) cc_final: 0.7081 (p90) REVERT: H 100 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.7951 (ttm110) REVERT: I 93 MET cc_start: 0.7885 (mmt) cc_final: 0.7607 (mmt) REVERT: I 183 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7327 (mt-10) REVERT: I 196 PHE cc_start: 0.8464 (m-80) cc_final: 0.8042 (m-10) outliers start: 30 outliers final: 17 residues processed: 280 average time/residue: 0.2495 time to fit residues: 98.1352 Evaluate side-chains 261 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL 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: 0.0470 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.0270 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 3.2142 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN E 44 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12537 Z= 0.252 Angle : 0.774 17.023 17001 Z= 0.400 Chirality : 0.043 0.227 2143 Planarity : 0.004 0.050 2174 Dihedral : 4.937 31.913 1773 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.53 % Allowed : 25.54 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.20), residues: 1709 helix: 1.10 (0.19), residues: 749 sheet: 0.29 (0.37), residues: 205 loop : -1.15 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.002 PHE E 196 TYR 0.024 0.002 TYR F 133 ARG 0.010 0.001 ARG D 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 291 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 1.414 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 129 ASP cc_start: 0.8550 (m-30) cc_final: 0.8167 (m-30) REVERT: A 173 ASN cc_start: 0.8430 (t0) cc_final: 0.8078 (p0) REVERT: B 83 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8046 (mp0) REVERT: B 96 PHE cc_start: 0.7905 (m-80) cc_final: 0.7700 (m-10) REVERT: C 33 MET cc_start: 0.8796 (tmm) cc_final: 0.8476 (tmm) REVERT: C 131 PHE cc_start: 0.7000 (m-80) cc_final: 0.6759 (m-10) REVERT: C 196 PHE cc_start: 0.8614 (m-10) cc_final: 0.8040 (m-80) REVERT: E 35 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8370 (ttmm) REVERT: E 196 PHE cc_start: 0.8089 (m-10) cc_final: 0.7755 (m-80) REVERT: F 44 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7827 (tm-30) REVERT: F 62 ASP cc_start: 0.8503 (p0) cc_final: 0.7988 (p0) REVERT: G 38 GLN cc_start: 0.8816 (tp40) cc_final: 0.8517 (tp-100) REVERT: G 49 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8425 (mm110) REVERT: G 96 PHE cc_start: 0.7123 (m-80) cc_final: 0.6837 (m-10) REVERT: H 83 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7971 (tp30) REVERT: H 100 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7919 (ttm110) REVERT: I 93 MET cc_start: 0.7797 (mmt) cc_final: 0.7491 (mmt) REVERT: I 183 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7318 (mt-10) REVERT: I 196 PHE cc_start: 0.8477 (m-80) cc_final: 0.8032 (m-10) outliers start: 33 outliers final: 23 residues processed: 285 average time/residue: 0.2648 time to fit residues: 106.7196 Evaluate side-chains 272 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL 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: 4.9990 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 0.0040 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 0.0670 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 overall best weight: 1.7334 ------------------------------------------------------------------------------- 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 ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN C 44 GLN D 117 GLN E 44 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12537 Z= 0.219 Angle : 0.767 15.930 17001 Z= 0.394 Chirality : 0.043 0.178 2143 Planarity : 0.004 0.052 2174 Dihedral : 4.820 28.725 1773 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.99 % Allowed : 26.61 % Favored : 71.40 % 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: 0.12 (0.21), residues: 1709 helix: 1.18 (0.19), residues: 749 sheet: 0.35 (0.37), residues: 205 loop : -1.12 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE H 131 TYR 0.021 0.002 TYR F 133 ARG 0.011 0.001 ARG D 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 282 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 1.404 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 129 ASP cc_start: 0.8489 (m-30) cc_final: 0.8073 (m-30) REVERT: A 173 ASN cc_start: 0.8422 (t0) cc_final: 0.8062 (p0) REVERT: B 33 MET cc_start: 0.8244 (mmm) cc_final: 0.7792 (mmm) REVERT: B 83 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8061 (mp0) REVERT: B 96 PHE cc_start: 0.7899 (m-80) cc_final: 0.7565 (m-80) REVERT: C 33 MET cc_start: 0.8815 (tmm) cc_final: 0.8540 (tmm) REVERT: C 131 PHE cc_start: 0.6934 (m-80) cc_final: 0.5958 (m-80) REVERT: C 196 PHE cc_start: 0.8549 (m-10) cc_final: 0.8314 (m-80) REVERT: D 32 ASN cc_start: 0.8602 (m-40) cc_final: 0.8097 (t0) REVERT: D 92 ASN cc_start: 0.8780 (t0) cc_final: 0.8571 (t0) REVERT: E 2 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8164 (p) REVERT: E 83 GLU cc_start: 0.8701 (tp30) cc_final: 0.8128 (tp30) REVERT: E 196 PHE cc_start: 0.8019 (m-10) cc_final: 0.7692 (m-80) REVERT: F 44 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7815 (tm-30) REVERT: F 62 ASP cc_start: 0.8450 (p0) cc_final: 0.7917 (p0) REVERT: F 93 MET cc_start: 0.8595 (mmm) cc_final: 0.8141 (mmm) REVERT: G 38 GLN cc_start: 0.8791 (tp40) cc_final: 0.8474 (tp-100) REVERT: G 96 PHE cc_start: 0.7090 (m-80) cc_final: 0.6813 (m-10) REVERT: H 83 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7916 (tp30) REVERT: H 98 PHE cc_start: 0.7485 (p90) cc_final: 0.7171 (p90) REVERT: H 100 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7930 (ttm110) REVERT: I 93 MET cc_start: 0.7774 (mmt) cc_final: 0.7540 (mmt) REVERT: I 183 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7356 (mt-10) REVERT: I 196 PHE cc_start: 0.8458 (m-80) cc_final: 0.8015 (m-10) outliers start: 26 outliers final: 22 residues processed: 278 average time/residue: 0.2745 time to fit residues: 106.3197 Evaluate side-chains 267 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 194 VAL 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 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 49 GLN 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: 5.9990 chunk 76 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN E 44 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12537 Z= 0.397 Angle : 0.897 17.674 17001 Z= 0.467 Chirality : 0.046 0.230 2143 Planarity : 0.005 0.062 2174 Dihedral : 5.567 35.022 1773 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.30 % Allowed : 26.84 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1709 helix: 0.64 (0.19), residues: 744 sheet: 0.28 (0.37), residues: 203 loop : -1.35 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.045 0.003 PHE E 196 TYR 0.028 0.003 TYR F 133 ARG 0.008 0.001 ARG D 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 282 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 252 time to evaluate : 1.552 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: B 83 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8083 (mp0) REVERT: B 96 PHE cc_start: 0.7943 (m-80) cc_final: 0.7561 (m-80) REVERT: E 35 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8314 (ttmm) REVERT: E 93 MET cc_start: 0.6981 (mtt) cc_final: 0.6721 (mtt) REVERT: F 44 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7992 (tm-30) REVERT: F 93 MET cc_start: 0.8728 (mmm) cc_final: 0.8338 (mmm) REVERT: G 52 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8702 (mmm160) REVERT: G 96 PHE cc_start: 0.7222 (m-80) cc_final: 0.6943 (m-10) REVERT: H 38 GLN cc_start: 0.8809 (mt0) cc_final: 0.8544 (mt0) REVERT: H 83 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8010 (tp30) REVERT: H 98 PHE cc_start: 0.7663 (p90) cc_final: 0.7349 (p90) REVERT: H 100 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.7947 (ttm110) REVERT: I 93 MET cc_start: 0.7741 (mmt) cc_final: 0.7511 (mmt) REVERT: I 183 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7494 (mt-10) REVERT: I 196 PHE cc_start: 0.8512 (m-80) cc_final: 0.8140 (m-10) outliers start: 30 outliers final: 24 residues processed: 276 average time/residue: 0.2594 time to fit residues: 100.2990 Evaluate side-chains 270 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 6 VAL 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 41 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 49 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN D 117 GLN E 44 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 119 GLN ** 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 = 0.3287 r_free = 0.3287 target = 0.049327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.042299 restraints weight = 82661.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.043441 restraints weight = 48285.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.044224 restraints weight = 32173.846| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12537 Z= 0.290 Angle : 0.847 16.199 17001 Z= 0.436 Chirality : 0.044 0.174 2143 Planarity : 0.005 0.064 2174 Dihedral : 5.421 32.213 1773 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.30 % Allowed : 27.53 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.33 (0.20), residues: 1709 helix: 0.74 (0.19), residues: 749 sheet: 0.26 (0.37), residues: 204 loop : -1.33 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE E 196 TYR 0.028 0.002 TYR F 133 ARG 0.006 0.001 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.99 seconds wall clock time: 57 minutes 53.17 seconds (3473.17 seconds total)