Starting phenix.real_space_refine on Fri Mar 15 06:44:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxl_24073/03_2024/7mxl_24073.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 37 5.16 5 C 6850 2.51 5 N 1817 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "J ASP 151": "OD1" <-> "OD2" Residue "J TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 206": "OD1" <-> "OD2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ASP 171": "OD1" <-> "OD2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "H ASP 10": "OD1" <-> "OD2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10866 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1553 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1554 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1233 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 150} Chain: "J" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1618 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 2 Chain: "K" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1650 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1626 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206} Time building chain proxies: 6.18, per 1000 atoms: 0.57 Number of scatterers: 10866 At special positions: 0 Unit cell: (114.4, 148.72, 144.56, 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 37 16.00 O 2162 8.00 N 1817 7.00 C 6850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS K 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " 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: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 34 sheets defined 9.6% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.677A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.573A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 25 through 28 removed outlier: 4.588A pdb=" N ASP C 28 " --> pdb=" O LEU C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 28' Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 130 through 155 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.624A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.028A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 32 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.980A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 129 Processing helix chain 'K' and resid 184 through 188 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.547A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.532A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.512A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.862A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.793A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.592A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 51 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP A 35 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.592A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 51 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP A 35 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.036A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.036A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158 removed outlier: 3.542A pdb=" N THR A 155 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 7.009A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 12 removed outlier: 3.875A pdb=" N LYS C 98 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N GLU C 97 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU C 88 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS C 69 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY C 89 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR C 67 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 54 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 12 removed outlier: 3.875A pdb=" N LYS C 98 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N GLU C 97 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU C 88 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.470A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.276A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.198A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.198A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.773A pdb=" N LEU K 13 " --> pdb=" O GLU K 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.428A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 118 through 119 removed outlier: 3.676A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 145 through 151 removed outlier: 4.020A pdb=" N LYS K 146 " --> pdb=" O THR K 198 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR K 193 " --> pdb=" O PHE K 210 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.231A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.231A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.573A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.630A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.844A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.724A pdb=" N ASN H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.883A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.883A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 157 through 160 512 hydrogen bonds defined for protein. 1281 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: 3.75 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3469 1.34 - 1.46: 2735 1.46 - 1.58: 4872 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 11121 Sorted by residual: bond pdb=" CG1 ILE H 101 " pdb=" CD1 ILE H 101 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.79e-01 bond pdb=" CA ASN A 208 " pdb=" CB ASN A 208 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.65e-01 bond pdb=" CG1 ILE C 92 " pdb=" CD1 ILE C 92 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.86e-01 bond pdb=" CB ASN A 208 " pdb=" CG ASN A 208 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.42e-01 bond pdb=" CB LYS A 205 " pdb=" CG LYS A 205 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.96e-01 ... (remaining 11116 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 268 105.88 - 112.90: 6054 112.90 - 119.93: 3410 119.93 - 126.95: 5246 126.95 - 133.98: 146 Bond angle restraints: 15124 Sorted by residual: angle pdb=" C GLU J 155 " pdb=" N PRO J 156 " pdb=" CD PRO J 156 " ideal model delta sigma weight residual 120.60 114.33 6.27 2.20e+00 2.07e-01 8.13e+00 angle pdb=" N ILE J 30 " pdb=" CA ILE J 30 " pdb=" C ILE J 30 " ideal model delta sigma weight residual 113.00 109.36 3.64 1.30e+00 5.92e-01 7.85e+00 angle pdb=" N LYS A 121 " pdb=" CA LYS A 121 " pdb=" C LYS A 121 " ideal model delta sigma weight residual 108.34 111.90 -3.56 1.31e+00 5.83e-01 7.39e+00 angle pdb=" C SER A 207 " pdb=" N ASN A 208 " pdb=" CA ASN A 208 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.57e+00 angle pdb=" C GLN J 178 " pdb=" N SER J 179 " pdb=" CA SER J 179 " ideal model delta sigma weight residual 120.60 124.62 -4.02 1.60e+00 3.91e-01 6.30e+00 ... (remaining 15119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6067 17.58 - 35.16: 464 35.16 - 52.74: 83 52.74 - 70.31: 16 70.31 - 87.89: 10 Dihedral angle restraints: 6640 sinusoidal: 2530 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.38 43.62 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA GLN J 178 " pdb=" C GLN J 178 " pdb=" N SER J 179 " pdb=" CA SER J 179 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS K 135 " pdb=" SG CYS K 135 " pdb=" SG CYS K 195 " pdb=" CB CYS K 195 " ideal model delta sinusoidal sigma weight residual 93.00 134.90 -41.90 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 6637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1048 0.034 - 0.067: 428 0.067 - 0.101: 158 0.101 - 0.135: 58 0.135 - 0.168: 8 Chirality restraints: 1700 Sorted by residual: chirality pdb=" CB THR K 10 " pdb=" CA THR K 10 " pdb=" OG1 THR K 10 " pdb=" CG2 THR K 10 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CG LEU A 19 " pdb=" CB LEU A 19 " pdb=" CD1 LEU A 19 " pdb=" CD2 LEU A 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1697 not shown) Planarity restraints: 1933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 155 " 0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO J 156 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO J 156 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO J 156 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO H 14 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 152 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO H 153 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " -0.021 5.00e-02 4.00e+02 ... (remaining 1930 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 239 2.67 - 3.22: 10207 3.22 - 3.78: 16757 3.78 - 4.34: 23800 4.34 - 4.90: 39668 Nonbonded interactions: 90671 Sorted by model distance: nonbonded pdb=" OD2 ASP B 105 " pdb=" OH TYR B 173 " model vdw 2.106 2.440 nonbonded pdb=" OE2 GLU C 102 " pdb=" OH TYR L 49 " model vdw 2.146 2.440 nonbonded pdb=" NE2 GLN J 178 " pdb=" OG SER J 180 " model vdw 2.165 2.520 nonbonded pdb=" O TYR K 187 " pdb=" OH TYR K 193 " model vdw 2.173 2.440 nonbonded pdb=" NH1 ARG H 98 " pdb=" OD1 ASN H 108 " model vdw 2.204 2.520 ... (remaining 90666 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 'B' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59 \ or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 101 through 104 or resid 106 through 210)) selection = (chain 'K' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ resid 14 through 28 or resid 31 or resid 34 through 37 or resid 39 through 46 o \ r resid 48 through 50 or resid 52 through 53 or resid 55 or resid 57 through 60 \ or resid 62 through 70 or resid 72 through 76 or resid 79 or resid 82 through 85 \ or resid 87 or resid 89 or resid 91 or resid 96 or resid 98 through 100 or resi \ d 102 through 105 or resid 107 through 149 or resid 160 through 211)) selection = (chain 'L' and (resid 2 through 3 or resid 5 through 8 or resid 10 through 12 or \ resid 14 through 28 or resid 31 or resid 33 through 36 or resid 38 through 45 o \ r resid 47 through 49 or resid 51 through 52 or resid 54 or resid 56 through 59 \ or resid 61 through 69 or resid 71 through 75 or resid 78 or resid 81 through 84 \ or resid 86 or resid 88 or resid 90 or resid 95 or resid 97 through 99 or resid \ 101 through 104 or resid 106 through 148 or resid 159 through 210)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 2.940 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.750 Find NCS groups from input model: 0.620 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.004 0.045 11121 Z= 0.237 Angle : 0.612 7.625 15124 Z= 0.333 Chirality : 0.045 0.168 1700 Planarity : 0.005 0.097 1933 Dihedral : 13.075 87.893 3970 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.92 (0.22), residues: 1400 helix: -0.59 (0.57), residues: 83 sheet: -1.13 (0.20), residues: 646 loop : -1.39 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 158 HIS 0.003 0.001 HIS L 89 PHE 0.015 0.001 PHE A 79 TYR 0.019 0.001 TYR L 186 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: J 145 LEU cc_start: 0.8710 (mt) cc_final: 0.8461 (mt) REVERT: J 152 TYR cc_start: 0.7908 (p90) cc_final: 0.7511 (p90) REVERT: J 204 ASN cc_start: 0.7890 (p0) cc_final: 0.7489 (p0) REVERT: K 80 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7866 (mt-10) REVERT: K 140 PHE cc_start: 0.8928 (p90) cc_final: 0.8463 (p90) REVERT: K 143 ARG cc_start: 0.8375 (ttt-90) cc_final: 0.7987 (tpt90) REVERT: H 73 ASP cc_start: 0.8279 (t0) cc_final: 0.7849 (t70) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2792 time to fit residues: 65.7701 Evaluate side-chains 145 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11121 Z= 0.259 Angle : 0.567 7.524 15124 Z= 0.294 Chirality : 0.044 0.152 1700 Planarity : 0.005 0.073 1933 Dihedral : 4.749 71.419 1526 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.14 % Allowed : 6.94 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.71 (0.22), residues: 1400 helix: -0.25 (0.58), residues: 86 sheet: -0.93 (0.20), residues: 640 loop : -1.37 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.003 0.001 HIS L 89 PHE 0.017 0.002 PHE H 128 TYR 0.016 0.001 TYR K 92 ARG 0.012 0.001 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: J 43 GLN cc_start: 0.8151 (mm110) cc_final: 0.7951 (mm110) REVERT: J 145 LEU cc_start: 0.8685 (mt) cc_final: 0.8417 (mt) REVERT: K 78 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.7020 (mmm-85) REVERT: K 117 PHE cc_start: 0.8485 (m-80) cc_final: 0.8008 (m-80) REVERT: K 143 ARG cc_start: 0.8425 (ttt-90) cc_final: 0.8063 (tpt90) REVERT: K 180 LEU cc_start: 0.8331 (tp) cc_final: 0.7848 (mt) REVERT: H 73 ASP cc_start: 0.8156 (t0) cc_final: 0.7949 (t70) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.2667 time to fit residues: 59.6231 Evaluate side-chains 152 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 119 ASN ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 11121 Z= 0.413 Angle : 0.607 8.427 15124 Z= 0.318 Chirality : 0.045 0.158 1700 Planarity : 0.005 0.083 1933 Dihedral : 4.904 70.459 1526 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.04 % Allowed : 9.31 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.81 (0.22), residues: 1400 helix: -0.20 (0.59), residues: 86 sheet: -1.04 (0.19), residues: 656 loop : -1.39 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 161 HIS 0.005 0.001 HIS L 89 PHE 0.017 0.002 PHE C 23 TYR 0.019 0.002 TYR L 91 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: C 126 ASP cc_start: 0.7601 (t0) cc_final: 0.7400 (t0) REVERT: J 145 LEU cc_start: 0.8693 (mt) cc_final: 0.8410 (mt) REVERT: K 117 PHE cc_start: 0.8507 (m-80) cc_final: 0.8027 (m-80) REVERT: K 140 PHE cc_start: 0.8926 (p90) cc_final: 0.8459 (p90) REVERT: K 143 ARG cc_start: 0.8453 (ttt-90) cc_final: 0.8003 (tpt90) REVERT: L 134 CYS cc_start: 0.6119 (t) cc_final: 0.5684 (t) REVERT: L 158 ASN cc_start: 0.9000 (p0) cc_final: 0.8751 (p0) REVERT: L 189 HIS cc_start: 0.8073 (m170) cc_final: 0.7827 (m170) REVERT: L 210 ASN cc_start: 0.8450 (m-40) cc_final: 0.8082 (m-40) REVERT: H 73 ASP cc_start: 0.8131 (t0) cc_final: 0.7876 (t70) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.2598 time to fit residues: 59.0554 Evaluate side-chains 166 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.0980 chunk 95 optimal weight: 30.0000 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11121 Z= 0.219 Angle : 0.544 6.900 15124 Z= 0.281 Chirality : 0.043 0.150 1700 Planarity : 0.004 0.084 1933 Dihedral : 4.738 70.860 1526 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.04 % Allowed : 11.93 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.51 (0.22), residues: 1400 helix: 0.12 (0.60), residues: 85 sheet: -0.73 (0.20), residues: 632 loop : -1.33 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 161 HIS 0.003 0.001 HIS L 89 PHE 0.014 0.001 PHE A 79 TYR 0.017 0.001 TYR H 151 ARG 0.006 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 145 LEU cc_start: 0.8678 (mt) cc_final: 0.8412 (mt) REVERT: K 117 PHE cc_start: 0.8468 (m-80) cc_final: 0.8082 (m-80) REVERT: K 143 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.8185 (tpt90) REVERT: K 174 TYR cc_start: 0.7390 (m-10) cc_final: 0.7167 (m-10) REVERT: L 134 CYS cc_start: 0.6264 (t) cc_final: 0.5982 (t) REVERT: L 158 ASN cc_start: 0.8923 (p0) cc_final: 0.8639 (p0) REVERT: L 210 ASN cc_start: 0.8347 (m-40) cc_final: 0.8043 (m-40) REVERT: H 73 ASP cc_start: 0.8044 (t0) cc_final: 0.7820 (t70) outliers start: 25 outliers final: 19 residues processed: 174 average time/residue: 0.2635 time to fit residues: 62.6083 Evaluate side-chains 164 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11121 Z= 0.437 Angle : 0.615 8.801 15124 Z= 0.322 Chirality : 0.045 0.162 1700 Planarity : 0.005 0.092 1933 Dihedral : 4.923 70.122 1526 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.37 % Allowed : 13.56 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.63 (0.22), residues: 1400 helix: -0.07 (0.59), residues: 86 sheet: -0.92 (0.19), residues: 660 loop : -1.28 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 161 HIS 0.006 0.001 HIS L 89 PHE 0.018 0.002 PHE C 63 TYR 0.019 0.002 TYR L 91 ARG 0.008 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: J 145 LEU cc_start: 0.8706 (mt) cc_final: 0.8445 (mt) REVERT: J 189 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (m) REVERT: K 78 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7284 (mmm-85) REVERT: K 117 PHE cc_start: 0.8480 (m-80) cc_final: 0.8072 (m-80) REVERT: K 168 ASP cc_start: 0.8605 (t0) cc_final: 0.8405 (t0) REVERT: K 180 LEU cc_start: 0.8262 (tp) cc_final: 0.7992 (mp) REVERT: L 134 CYS cc_start: 0.6491 (t) cc_final: 0.6222 (t) REVERT: L 158 ASN cc_start: 0.8885 (p0) cc_final: 0.8568 (p0) REVERT: L 199 GLN cc_start: 0.8482 (tt0) cc_final: 0.8269 (pt0) REVERT: L 210 ASN cc_start: 0.8523 (m-40) cc_final: 0.8147 (m-40) REVERT: L 211 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7092 (mtm180) REVERT: H 73 ASP cc_start: 0.8089 (t0) cc_final: 0.7857 (t70) outliers start: 29 outliers final: 23 residues processed: 168 average time/residue: 0.2590 time to fit residues: 59.4804 Evaluate side-chains 165 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 0.1980 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11121 Z= 0.282 Angle : 0.567 7.399 15124 Z= 0.294 Chirality : 0.044 0.174 1700 Planarity : 0.005 0.092 1933 Dihedral : 4.838 70.524 1526 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.70 % Allowed : 14.95 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.50 (0.22), residues: 1400 helix: 0.18 (0.60), residues: 85 sheet: -0.81 (0.20), residues: 656 loop : -1.23 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 161 HIS 0.003 0.001 HIS L 89 PHE 0.015 0.001 PHE H 128 TYR 0.019 0.001 TYR H 151 ARG 0.008 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: J 145 LEU cc_start: 0.8706 (mt) cc_final: 0.8460 (mt) REVERT: J 189 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8334 (m) REVERT: K 117 PHE cc_start: 0.8446 (m-80) cc_final: 0.8046 (m-80) REVERT: K 143 ARG cc_start: 0.8406 (ttt-90) cc_final: 0.7932 (tpt90) REVERT: K 168 ASP cc_start: 0.8652 (t0) cc_final: 0.8402 (t0) REVERT: K 180 LEU cc_start: 0.8316 (tp) cc_final: 0.8025 (mp) REVERT: L 158 ASN cc_start: 0.8876 (p0) cc_final: 0.8575 (p0) REVERT: L 199 GLN cc_start: 0.8465 (tt0) cc_final: 0.8257 (pt0) REVERT: L 210 ASN cc_start: 0.8474 (m-40) cc_final: 0.8114 (m-40) REVERT: H 73 ASP cc_start: 0.8115 (t0) cc_final: 0.7859 (t70) outliers start: 33 outliers final: 23 residues processed: 168 average time/residue: 0.2541 time to fit residues: 59.0526 Evaluate side-chains 164 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11121 Z= 0.264 Angle : 0.564 7.076 15124 Z= 0.292 Chirality : 0.044 0.161 1700 Planarity : 0.005 0.093 1933 Dihedral : 4.785 70.647 1526 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.53 % Allowed : 14.87 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.40 (0.22), residues: 1400 helix: 0.30 (0.60), residues: 85 sheet: -0.77 (0.20), residues: 662 loop : -1.15 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 97 HIS 0.004 0.001 HIS L 89 PHE 0.016 0.001 PHE H 128 TYR 0.016 0.001 TYR K 92 ARG 0.009 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6521 (tmt170) cc_final: 0.5902 (tmt170) REVERT: J 145 LEU cc_start: 0.8718 (mt) cc_final: 0.8489 (mt) REVERT: K 117 PHE cc_start: 0.8441 (m-80) cc_final: 0.8051 (m-80) REVERT: K 143 ARG cc_start: 0.8418 (ttt-90) cc_final: 0.7952 (tpt90) REVERT: K 168 ASP cc_start: 0.8634 (t0) cc_final: 0.8300 (t0) REVERT: L 158 ASN cc_start: 0.8830 (p0) cc_final: 0.8500 (p0) REVERT: L 199 GLN cc_start: 0.8446 (tt0) cc_final: 0.8235 (pt0) REVERT: L 210 ASN cc_start: 0.8379 (m-40) cc_final: 0.8026 (m-40) REVERT: H 73 ASP cc_start: 0.8099 (t0) cc_final: 0.7838 (t70) outliers start: 31 outliers final: 25 residues processed: 166 average time/residue: 0.2517 time to fit residues: 57.7390 Evaluate side-chains 160 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11121 Z= 0.369 Angle : 0.596 8.020 15124 Z= 0.311 Chirality : 0.044 0.163 1700 Planarity : 0.005 0.097 1933 Dihedral : 4.887 70.432 1526 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.37 % Allowed : 15.20 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.45 (0.22), residues: 1400 helix: 0.22 (0.60), residues: 85 sheet: -0.78 (0.20), residues: 662 loop : -1.20 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 149 HIS 0.005 0.001 HIS L 89 PHE 0.016 0.002 PHE A 79 TYR 0.016 0.002 TYR L 91 ARG 0.009 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6529 (tmt170) cc_final: 0.5948 (tmt170) REVERT: J 145 LEU cc_start: 0.8715 (mt) cc_final: 0.8494 (mt) REVERT: K 117 PHE cc_start: 0.8436 (m-80) cc_final: 0.8035 (m-80) REVERT: K 140 PHE cc_start: 0.8842 (p90) cc_final: 0.8483 (p90) REVERT: K 143 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7931 (tpt90) REVERT: K 168 ASP cc_start: 0.8652 (t0) cc_final: 0.8360 (t0) REVERT: K 180 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8186 (mm) REVERT: L 158 ASN cc_start: 0.8814 (p0) cc_final: 0.8461 (p0) REVERT: L 199 GLN cc_start: 0.8495 (tt0) cc_final: 0.8285 (pt0) REVERT: L 210 ASN cc_start: 0.8380 (m-40) cc_final: 0.8046 (m-40) REVERT: H 73 ASP cc_start: 0.8129 (t0) cc_final: 0.7863 (t70) outliers start: 29 outliers final: 26 residues processed: 162 average time/residue: 0.2642 time to fit residues: 58.2925 Evaluate side-chains 162 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11121 Z= 0.227 Angle : 0.559 7.045 15124 Z= 0.289 Chirality : 0.043 0.155 1700 Planarity : 0.005 0.097 1933 Dihedral : 4.769 70.818 1526 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 2.21 % Allowed : 15.60 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.30 (0.23), residues: 1400 helix: 0.42 (0.61), residues: 85 sheet: -0.67 (0.20), residues: 662 loop : -1.12 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 161 HIS 0.005 0.001 HIS L 89 PHE 0.017 0.001 PHE H 128 TYR 0.013 0.001 TYR K 92 ARG 0.010 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.276 Fit side-chains REVERT: A 133 ARG cc_start: 0.6574 (tmt170) cc_final: 0.6004 (tmt170) REVERT: J 145 LEU cc_start: 0.8693 (mt) cc_final: 0.8452 (mt) REVERT: K 78 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7214 (mmm-85) REVERT: K 117 PHE cc_start: 0.8410 (m-80) cc_final: 0.8036 (m-80) REVERT: K 140 PHE cc_start: 0.8773 (p90) cc_final: 0.8443 (p90) REVERT: K 143 ARG cc_start: 0.8400 (ttt-90) cc_final: 0.7942 (tpt90) REVERT: K 168 ASP cc_start: 0.8645 (t0) cc_final: 0.8240 (t0) REVERT: L 158 ASN cc_start: 0.8773 (p0) cc_final: 0.8462 (p0) REVERT: L 210 ASN cc_start: 0.8246 (m-40) cc_final: 0.7946 (m-40) REVERT: H 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7859 (t70) outliers start: 27 outliers final: 23 residues processed: 158 average time/residue: 0.2581 time to fit residues: 55.9732 Evaluate side-chains 160 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN H 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 11121 Z= 0.606 Angle : 0.699 10.031 15124 Z= 0.367 Chirality : 0.047 0.180 1700 Planarity : 0.005 0.101 1933 Dihedral : 5.183 69.620 1526 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.36 % Favored : 91.50 % Rotamer: Outliers : 2.04 % Allowed : 16.18 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.66 (0.22), residues: 1400 helix: -0.11 (0.58), residues: 86 sheet: -0.89 (0.20), residues: 647 loop : -1.35 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 161 HIS 0.005 0.001 HIS C 122 PHE 0.023 0.002 PHE C 63 TYR 0.022 0.002 TYR B 49 ARG 0.011 0.001 ARG K 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.362 Fit side-chains REVERT: A 133 ARG cc_start: 0.6528 (tmt170) cc_final: 0.5963 (tmt170) REVERT: J 43 GLN cc_start: 0.8392 (mm110) cc_final: 0.8187 (mm110) REVERT: K 78 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7210 (mmm-85) REVERT: K 117 PHE cc_start: 0.8454 (m-80) cc_final: 0.8033 (m-80) REVERT: K 168 ASP cc_start: 0.8687 (t0) cc_final: 0.8407 (t0) REVERT: L 158 ASN cc_start: 0.8880 (p0) cc_final: 0.8410 (p0) REVERT: L 213 GLU cc_start: 0.7566 (pm20) cc_final: 0.7319 (pm20) REVERT: H 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7912 (t70) REVERT: H 212 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8393 (mmmm) REVERT: H 216 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7252 (tmt-80) outliers start: 25 outliers final: 22 residues processed: 161 average time/residue: 0.2503 time to fit residues: 55.9984 Evaluate side-chains 158 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 113 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN H 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070922 restraints weight = 20276.517| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.36 r_work: 0.2871 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11121 Z= 0.204 Angle : 0.580 7.323 15124 Z= 0.299 Chirality : 0.043 0.153 1700 Planarity : 0.005 0.097 1933 Dihedral : 4.881 70.435 1526 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 1.80 % Allowed : 16.67 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.34 (0.22), residues: 1400 helix: 0.33 (0.60), residues: 85 sheet: -0.67 (0.20), residues: 645 loop : -1.17 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 161 HIS 0.005 0.001 HIS L 89 PHE 0.021 0.001 PHE K 140 TYR 0.018 0.001 TYR H 151 ARG 0.010 0.001 ARG K 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.00 seconds wall clock time: 49 minutes 5.85 seconds (2945.85 seconds total)