Starting phenix.real_space_refine on Sat Dec 9 21:27:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/12_2023/8uhf_42279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/12_2023/8uhf_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_42279/12_2023/8uhf_42279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/12_2023/8uhf_42279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/12_2023/8uhf_42279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhf_42279/12_2023/8uhf_42279.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.121 sd= 0.873 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 7833 2.51 5 N 2083 2.21 5 O 2434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.11, per 1000 atoms: 0.57 Number of scatterers: 12411 At special positions: 0 Unit cell: (96.28, 96.28, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2434 8.00 N 2083 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 186 " distance=2.04 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS F 120 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 120 " - pdb=" SG CYS G 186 " distance=2.03 Simple disulfide: pdb=" SG CYS H 120 " - pdb=" SG CYS H 186 " distance=2.03 Simple disulfide: pdb=" SG CYS I 120 " - pdb=" SG CYS I 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 2.7 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: 1.16 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: 3.38 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4098 1.34 - 1.46: 2512 1.46 - 1.58: 5823 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 12537 Sorted by residual: bond pdb=" CG PRO G 191 " pdb=" CD PRO G 191 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.45e-01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.24e-01 bond pdb=" CB CYS E 120 " pdb=" SG CYS E 120 " ideal model delta sigma weight residual 1.808 1.781 0.027 3.30e-02 9.18e+02 6.89e-01 bond pdb=" C VAL D 127 " pdb=" O VAL D 127 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.15e-01 bond pdb=" CG PRO E 191 " pdb=" CD PRO E 191 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 5.96e-01 ... (remaining 12532 not shown) Histogram of bond angle deviations from ideal: 99.55 - 105.48: 201 105.48 - 111.41: 5817 111.41 - 117.34: 3475 117.34 - 123.27: 7228 123.27 - 129.21: 280 Bond angle restraints: 17001 Sorted by residual: angle pdb=" CA CYS C 120 " pdb=" CB CYS C 120 " pdb=" SG CYS C 120 " ideal model delta sigma weight residual 114.40 123.32 -8.92 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N ILE B 7 " pdb=" CA ILE B 7 " pdb=" C ILE B 7 " ideal model delta sigma weight residual 112.80 108.83 3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C LEU C 185 " pdb=" N CYS C 186 " pdb=" CA CYS C 186 " ideal model delta sigma weight residual 122.46 126.59 -4.13 1.41e+00 5.03e-01 8.56e+00 angle pdb=" C LEU A 3 " pdb=" N LEU A 4 " pdb=" CA LEU A 4 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.08e+00 angle pdb=" C CYS C 120 " pdb=" CA CYS C 120 " pdb=" CB CYS C 120 " ideal model delta sigma weight residual 110.84 106.92 3.92 1.66e+00 3.63e-01 5.56e+00 ... (remaining 16996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7104 17.91 - 35.81: 410 35.81 - 53.72: 60 53.72 - 71.63: 15 71.63 - 89.53: 10 Dihedral angle restraints: 7599 sinusoidal: 2686 harmonic: 4913 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 186 " pdb=" CB CYS A 186 " ideal model delta sinusoidal sigma weight residual -86.00 -136.43 50.43 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 120 " pdb=" SG CYS C 120 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual 93.00 129.75 -36.75 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS I 120 " pdb=" SG CYS I 120 " pdb=" SG CYS I 186 " pdb=" CB CYS I 186 " ideal model delta sinusoidal sigma weight residual 93.00 126.56 -33.56 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 7596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1280 0.026 - 0.052: 542 0.052 - 0.078: 206 0.078 - 0.105: 68 0.105 - 0.131: 47 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA ILE G 134 " pdb=" N ILE G 134 " pdb=" C ILE G 134 " pdb=" CB ILE G 134 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL E 112 " pdb=" N VAL E 112 " pdb=" C VAL E 112 " pdb=" CB VAL E 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE E 110 " pdb=" N ILE E 110 " pdb=" C ILE E 110 " pdb=" CB ILE E 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2140 not shown) Planarity restraints: 2174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 4 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C LEU A 4 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 4 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 5 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 9 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C VAL D 9 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 10 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 7 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C ILE B 7 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE B 7 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 2171 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 232 2.68 - 3.24: 12801 3.24 - 3.79: 19679 3.79 - 4.35: 25879 4.35 - 4.90: 42002 Nonbonded interactions: 100593 Sorted by model distance: nonbonded pdb=" OG SER B 39 " pdb=" O GLU B 83 " model vdw 2.126 2.440 nonbonded pdb=" OG SER A 39 " pdb=" O GLU A 83 " model vdw 2.202 2.440 nonbonded pdb=" OG SER F 80 " pdb=" OD1 ASP F 82 " model vdw 2.218 2.440 nonbonded pdb=" O ASP H 149 " pdb=" OG SER H 153 " model vdw 2.240 2.440 nonbonded pdb=" O GLY E 128 " pdb=" NZ LYS E 165 " model vdw 2.247 2.520 ... (remaining 100588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'B' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'C' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'D' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'E' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'F' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'G' and (resid 2 through 52 or resid 62 through 196)) selection = (chain 'H' and resid 2 through 196) selection = (chain 'I' and (resid 2 through 52 or resid 62 through 196)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.260 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- 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 : 1.632 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 outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3164 time to fit residues: 173.9465 Evaluate side-chains 280 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7704 ------------------------------------------------------------------------------- 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: 0.9990 chunk 128 optimal weight: 0.0060 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 92 ASN A 198 ASN C 44 GLN D 44 GLN D 94 ASN D 105 ASN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 25 GLN H 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN I 41 ASN I 49 GLN I 94 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2944 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= 0.199 Angle : 0.639 12.038 17001 Z= 0.333 Chirality : 0.041 0.147 2143 Planarity : 0.004 0.039 2174 Dihedral : 4.371 19.859 1773 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.84 % Allowed : 16.10 % Favored : 82.06 % 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: -0.53 (0.20), residues: 1709 helix: 0.90 (0.19), residues: 748 sheet: -0.51 (0.32), residues: 221 loop : -1.62 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE C 192 TYR 0.017 0.002 TYR C 133 ARG 0.006 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 342 time to evaluate : 1.623 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 outliers start: 24 outliers final: 15 residues processed: 353 average time/residue: 0.2914 time to fit residues: 140.8890 Evaluate side-chains 287 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1124 time to fit residues: 4.9254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 128 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN F 38 GLN G 56 ASN G 152 ASN G 198 ASN H 41 ASN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12537 Z= 0.264 Angle : 0.667 11.009 17001 Z= 0.354 Chirality : 0.042 0.194 2143 Planarity : 0.004 0.036 2174 Dihedral : 4.881 21.436 1773 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.38 % Allowed : 19.94 % Favored : 77.68 % 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: -0.26 (0.20), residues: 1709 helix: 0.96 (0.19), residues: 748 sheet: -0.26 (0.34), residues: 221 loop : -1.32 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.038 0.002 PHE E 196 TYR 0.016 0.002 TYR F 133 ARG 0.004 0.001 ARG G 52 *********************** 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: 31 poor density : 297 time to evaluate : 1.421 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 outliers start: 31 outliers final: 15 residues processed: 310 average time/residue: 0.2898 time to fit residues: 123.1775 Evaluate side-chains 264 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1394 time to fit residues: 5.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 94 ASN E 31 GLN E 44 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12537 Z= 0.220 Angle : 0.638 6.442 17001 Z= 0.336 Chirality : 0.041 0.152 2143 Planarity : 0.004 0.037 2174 Dihedral : 4.843 22.909 1773 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.99 % Allowed : 21.93 % Favored : 76.07 % 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: -0.12 (0.20), residues: 1709 helix: 1.04 (0.19), residues: 744 sheet: -0.16 (0.34), residues: 220 loop : -1.20 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE B 96 TYR 0.014 0.002 TYR C 133 ARG 0.008 0.001 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 1.481 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 outliers start: 26 outliers final: 12 residues processed: 293 average time/residue: 0.2671 time to fit residues: 108.5779 Evaluate side-chains 264 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1131 time to fit residues: 4.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 119 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN E 44 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4360 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= 0.227 Angle : 0.658 11.167 17001 Z= 0.342 Chirality : 0.041 0.151 2143 Planarity : 0.004 0.038 2174 Dihedral : 4.852 23.447 1773 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.38 % Allowed : 24.39 % Favored : 73.24 % 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: -0.04 (0.20), residues: 1709 helix: 1.15 (0.19), residues: 741 sheet: -0.03 (0.34), residues: 214 loop : -1.22 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE B 96 TYR 0.014 0.002 TYR G 57 ARG 0.005 0.001 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 1.318 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 outliers start: 31 outliers final: 15 residues processed: 291 average time/residue: 0.3180 time to fit residues: 127.5016 Evaluate side-chains 261 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1535 time to fit residues: 5.8191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12537 Z= 0.335 Angle : 0.750 11.710 17001 Z= 0.392 Chirality : 0.043 0.167 2143 Planarity : 0.004 0.041 2174 Dihedral : 5.410 25.066 1773 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.07 % Allowed : 26.38 % Favored : 71.55 % 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: -0.37 (0.20), residues: 1709 helix: 0.79 (0.18), residues: 739 sheet: -0.02 (0.35), residues: 203 loop : -1.34 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.043 0.002 PHE E 196 TYR 0.014 0.002 TYR G 51 ARG 0.007 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 1.517 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 outliers start: 27 outliers final: 12 residues processed: 286 average time/residue: 0.2531 time to fit residues: 103.1798 Evaluate side-chains 254 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1190 time to fit residues: 4.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12537 Z= 0.252 Angle : 0.726 15.244 17001 Z= 0.375 Chirality : 0.042 0.211 2143 Planarity : 0.004 0.049 2174 Dihedral : 5.204 25.815 1773 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.69 % Allowed : 27.53 % Favored : 70.78 % 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: -0.23 (0.20), residues: 1709 helix: 0.91 (0.19), residues: 742 sheet: -0.02 (0.35), residues: 205 loop : -1.26 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE B 96 TYR 0.014 0.002 TYR G 51 ARG 0.009 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 281 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 259 time to evaluate : 1.537 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 outliers start: 22 outliers final: 10 residues processed: 272 average time/residue: 0.2594 time to fit residues: 98.9386 Evaluate side-chains 255 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1210 time to fit residues: 3.9945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12537 Z= 0.341 Angle : 0.781 12.984 17001 Z= 0.408 Chirality : 0.043 0.188 2143 Planarity : 0.004 0.049 2174 Dihedral : 5.585 27.630 1773 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 28.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.69 % Allowed : 28.76 % Favored : 69.56 % 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: -0.55 (0.20), residues: 1709 helix: 0.60 (0.18), residues: 747 sheet: -0.07 (0.36), residues: 205 loop : -1.43 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE E 196 TYR 0.017 0.002 TYR G 51 ARG 0.009 0.001 ARG B 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 277 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 1.568 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 outliers start: 22 outliers final: 13 residues processed: 269 average time/residue: 0.3045 time to fit residues: 114.9857 Evaluate side-chains 251 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 1.510 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1524 time to fit residues: 5.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12537 Z= 0.250 Angle : 0.751 10.318 17001 Z= 0.389 Chirality : 0.042 0.157 2143 Planarity : 0.004 0.052 2174 Dihedral : 5.302 24.891 1773 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.77 % Allowed : 29.60 % Favored : 69.63 % 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: -0.30 (0.20), residues: 1709 helix: 0.88 (0.19), residues: 745 sheet: -0.18 (0.36), residues: 212 loop : -1.30 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE E 196 TYR 0.017 0.001 TYR G 51 ARG 0.009 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 264 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 254 time to evaluate : 1.416 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 outliers start: 10 outliers final: 7 residues processed: 259 average time/residue: 0.2777 time to fit residues: 100.2033 Evaluate side-chains 240 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1289 time to fit residues: 3.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12537 Z= 0.277 Angle : 0.784 12.596 17001 Z= 0.403 Chirality : 0.043 0.256 2143 Planarity : 0.004 0.055 2174 Dihedral : 5.326 26.032 1773 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.23 % Allowed : 30.83 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1709 helix: 0.91 (0.19), residues: 738 sheet: -0.14 (0.36), residues: 209 loop : -1.38 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE C 196 TYR 0.026 0.002 TYR E 133 ARG 0.011 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 243 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 1.388 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 outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.2734 time to fit residues: 92.2376 Evaluate side-chains 239 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1105 time to fit residues: 2.1386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.042442 restraints weight = 83141.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.043568 restraints weight = 49303.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044332 restraints weight = 33129.057| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12537 Z= 0.260 Angle : 0.778 10.179 17001 Z= 0.400 Chirality : 0.043 0.233 2143 Planarity : 0.004 0.056 2174 Dihedral : 5.301 26.307 1773 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.84 % Allowed : 30.60 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1709 helix: 0.91 (0.19), residues: 741 sheet: -0.11 (0.38), residues: 194 loop : -1.39 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE C 196 TYR 0.028 0.002 TYR E 133 ARG 0.015 0.001 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.48 seconds wall clock time: 53 minutes 59.22 seconds (3239.22 seconds total)