Starting phenix.real_space_refine on Wed Nov 15 10:28:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/11_2023/3jca_6441.pdb" } resolution = 4.8 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= 0.002 sd= 0.044 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 78 5.49 5 S 44 5.16 5 C 7086 2.51 5 N 2076 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11466 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "D" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "E" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 50.219 31.097 35.214 1.00117.64 S ATOM 320 SG CYS A 40 50.724 33.076 35.605 1.00129.65 S ATOM 2395 SG CYS B 37 120.732 24.422 25.373 1.00177.75 S ATOM 2416 SG CYS B 40 121.081 26.218 26.600 1.00174.63 S ATOM 5212 SG CYS E 37 91.196 65.853 35.151 1.00117.34 S ATOM 5233 SG CYS E 40 90.593 63.888 35.391 1.00131.03 S ATOM 7308 SG CYS F 37 20.729 72.530 25.394 1.00178.00 S ATOM 7329 SG CYS F 40 20.380 70.736 26.617 1.00174.87 S Time building chain proxies: 6.62, per 1000 atoms: 0.58 Number of scatterers: 11466 At special positions: 0 Unit cell: (142.79, 98.25, 94.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 44 16.00 P 78 15.00 O 2178 8.00 N 2076 7.00 C 7086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.08 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " Number of angles added : 6 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 39.2% alpha, 21.0% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 69 through 76 removed outlier: 7.147A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 174 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 150 through 171 Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.134A pdb=" N GLY B 175 " --> pdb=" O GLN B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 69 through 76 removed outlier: 7.143A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 174 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 209 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 150 through 171 Processing helix chain 'F' and resid 172 through 175 removed outlier: 4.085A pdb=" N GLY F 175 " --> pdb=" O GLN F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 202 through 209 Processing sheet with id= A, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.547A pdb=" N TYR A 77 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 254 through 257 removed outlier: 5.629A pdb=" N VAL A 219 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.545A pdb=" N TRP B 62 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 119 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 254 through 257 removed outlier: 5.600A pdb=" N VAL B 219 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET B 218 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 254 through 257 removed outlier: 5.370A pdb=" N VAL C 219 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 254 through 257 removed outlier: 6.598A pdb=" N TYR D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 238 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS D 244 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 231 " --> pdb=" O TRP D 221 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP D 221 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 88 through 94 removed outlier: 3.543A pdb=" N TYR E 77 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 254 through 257 removed outlier: 5.646A pdb=" N VAL E 219 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 89 through 94 removed outlier: 6.548A pdb=" N TRP F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 119 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 254 through 257 removed outlier: 5.595A pdb=" N VAL F 219 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET F 218 " --> pdb=" O PHE F 264 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 254 through 257 removed outlier: 5.364A pdb=" N VAL G 219 " --> pdb=" O PRO G 232 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.606A pdb=" N TYR H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA H 238 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS H 244 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 231 " --> pdb=" O TRP H 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP H 221 " --> pdb=" O GLY H 231 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2604 1.33 - 1.45: 3657 1.45 - 1.58: 5483 1.58 - 1.70: 154 1.70 - 1.82: 72 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP G 223 " pdb=" C ASP G 223 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ASP C 223 " pdb=" C ASP C 223 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" CA TRP A 208 " pdb=" CB TRP A 208 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.51e-02 4.39e+03 1.28e+01 bond pdb=" CA ARG A 27 " pdb=" C ARG A 27 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CA SER B 86 " pdb=" CB SER B 86 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.65e-02 3.67e+03 1.08e+01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.16: 702 105.16 - 112.34: 6161 112.34 - 119.52: 3811 119.52 - 126.71: 5512 126.71 - 133.89: 438 Bond angle restraints: 16624 Sorted by residual: angle pdb=" C PHE E 246 " pdb=" N PRO E 247 " pdb=" CA PRO E 247 " ideal model delta sigma weight residual 119.78 130.02 -10.24 1.03e+00 9.43e-01 9.88e+01 angle pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.78 129.93 -10.15 1.03e+00 9.43e-01 9.71e+01 angle pdb=" C PHE F 246 " pdb=" N PRO F 247 " pdb=" CA PRO F 247 " ideal model delta sigma weight residual 119.78 129.04 -9.26 1.03e+00 9.43e-01 8.09e+01 angle pdb=" C PHE B 246 " pdb=" N PRO B 247 " pdb=" CA PRO B 247 " ideal model delta sigma weight residual 119.78 128.99 -9.21 1.03e+00 9.43e-01 8.00e+01 angle pdb=" C LYS E 216 " pdb=" N PRO E 217 " pdb=" CA PRO E 217 " ideal model delta sigma weight residual 120.31 128.93 -8.62 9.80e-01 1.04e+00 7.74e+01 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 6269 31.88 - 63.77: 475 63.77 - 95.65: 18 95.65 - 127.54: 0 127.54 - 159.42: 2 Dihedral angle restraints: 6764 sinusoidal: 3202 harmonic: 3562 Sorted by residual: dihedral pdb=" C4' DA K 1 " pdb=" C3' DA K 1 " pdb=" O3' DA K 1 " pdb=" P DA K 2 " ideal model delta sinusoidal sigma weight residual 220.00 60.58 159.42 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DA I 1 " pdb=" C3' DA I 1 " pdb=" O3' DA I 1 " pdb=" P DA I 2 " ideal model delta sinusoidal sigma weight residual 220.00 64.50 155.50 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -131.24 8.64 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 6761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1284 0.073 - 0.147: 468 0.147 - 0.220: 36 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP E 208 " pdb=" N TRP E 208 " pdb=" C TRP E 208 " pdb=" CB TRP E 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TRP A 208 " pdb=" N TRP A 208 " pdb=" C TRP A 208 " pdb=" CB TRP A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1787 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 40 " -0.101 5.00e-02 4.00e+02 1.54e-01 3.82e+01 pdb=" N PRO E 41 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 40 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 41 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 265 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C THR A 265 " -0.063 2.00e-02 2.50e+03 pdb=" O THR A 265 " 0.023 2.00e-02 2.50e+03 pdb=" OXT THR A 265 " 0.022 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4253 2.88 - 3.38: 11041 3.38 - 3.89: 22227 3.89 - 4.39: 26011 4.39 - 4.90: 38001 Nonbonded interactions: 101533 Sorted by model distance: nonbonded pdb=" N GLU B 71 " pdb=" OE1 GLU B 71 " model vdw 2.370 2.520 nonbonded pdb=" N GLU F 71 " pdb=" OE1 GLU F 71 " model vdw 2.373 2.520 nonbonded pdb=" O5' DA K 2 " pdb=" O4' DA K 2 " model vdw 2.459 2.432 nonbonded pdb=" O PHE H 264 " pdb=" OG1 THR H 265 " model vdw 2.479 2.440 nonbonded pdb=" O PHE D 264 " pdb=" OG1 THR D 265 " model vdw 2.481 2.440 ... (remaining 101528 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 1 through 41 or resid 54 through 265 or resid 500)) selection = chain 'B' selection = (chain 'E' and (resid 1 through 41 or resid 54 through 265 or resid 500)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 1.030 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: 4.010 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 38.790 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.012 0.062 11970 Z= 0.787 Angle : 1.491 12.509 16624 Z= 1.038 Chirality : 0.067 0.367 1790 Planarity : 0.011 0.154 1856 Dihedral : 18.618 159.419 4452 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.87 (0.21), residues: 1202 helix: -0.84 (0.21), residues: 440 sheet: 0.23 (0.42), residues: 146 loop : -1.93 (0.22), residues: 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 411 average time/residue: 0.2738 time to fit residues: 150.7958 Evaluate side-chains 207 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 63 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 79 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11970 Z= 0.212 Angle : 0.645 7.232 16624 Z= 0.363 Chirality : 0.043 0.160 1790 Planarity : 0.006 0.068 1856 Dihedral : 23.542 151.681 2108 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.57 (0.23), residues: 1202 helix: 0.38 (0.24), residues: 420 sheet: 0.44 (0.44), residues: 146 loop : -1.09 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.128 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 outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2230 time to fit residues: 101.3404 Evaluate side-chains 183 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 68 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 195 ASN B 201 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 154 GLN F 12 HIS ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS F 192 ASN F 195 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11970 Z= 0.274 Angle : 0.661 6.067 16624 Z= 0.370 Chirality : 0.043 0.159 1790 Planarity : 0.006 0.057 1856 Dihedral : 23.378 148.132 2108 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.29 % Allowed : 2.12 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.28 (0.24), residues: 1202 helix: 0.70 (0.24), residues: 420 sheet: 0.00 (0.39), residues: 170 loop : -0.83 (0.26), residues: 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.187 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 outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.2110 time to fit residues: 77.0945 Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 201 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11970 Z= 0.209 Angle : 0.606 7.076 16624 Z= 0.338 Chirality : 0.042 0.140 1790 Planarity : 0.005 0.044 1856 Dihedral : 23.110 145.776 2108 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.09 (0.24), residues: 1202 helix: 0.85 (0.25), residues: 422 sheet: -0.12 (0.38), residues: 174 loop : -0.64 (0.26), residues: 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.205 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 outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1963 time to fit residues: 66.8911 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN F 79 HIS ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11970 Z= 0.291 Angle : 0.661 8.340 16624 Z= 0.367 Chirality : 0.043 0.185 1790 Planarity : 0.005 0.051 1856 Dihedral : 23.124 142.696 2108 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.25), residues: 1202 helix: 0.73 (0.25), residues: 424 sheet: -0.48 (0.38), residues: 176 loop : -0.78 (0.27), residues: 602 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.116 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 outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1859 time to fit residues: 58.2555 Evaluate side-chains 133 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 195 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11970 Z= 0.269 Angle : 0.647 5.979 16624 Z= 0.363 Chirality : 0.043 0.293 1790 Planarity : 0.005 0.048 1856 Dihedral : 23.107 141.313 2108 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.45 (0.24), residues: 1202 helix: 0.65 (0.25), residues: 424 sheet: -0.44 (0.37), residues: 178 loop : -0.91 (0.26), residues: 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.108 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 outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2051 time to fit residues: 59.6596 Evaluate side-chains 126 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11970 Z= 0.195 Angle : 0.594 6.989 16624 Z= 0.331 Chirality : 0.042 0.162 1790 Planarity : 0.005 0.041 1856 Dihedral : 22.904 139.554 2108 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.28 (0.25), residues: 1202 helix: 0.88 (0.26), residues: 426 sheet: -0.29 (0.41), residues: 146 loop : -0.89 (0.26), residues: 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.260 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 outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2124 time to fit residues: 62.9767 Evaluate side-chains 131 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 108 optimal weight: 0.0670 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11970 Z= 0.180 Angle : 0.595 7.605 16624 Z= 0.332 Chirality : 0.042 0.166 1790 Planarity : 0.005 0.037 1856 Dihedral : 22.777 137.781 2108 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.19 % Allowed : 1.16 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.27 (0.25), residues: 1202 helix: 0.87 (0.26), residues: 426 sheet: -0.73 (0.36), residues: 186 loop : -0.71 (0.27), residues: 590 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.149 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 outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2037 time to fit residues: 61.2616 Evaluate side-chains 135 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.0020 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11970 Z= 0.181 Angle : 0.601 9.189 16624 Z= 0.333 Chirality : 0.043 0.214 1790 Planarity : 0.005 0.067 1856 Dihedral : 22.731 137.105 2108 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.15 (0.25), residues: 1202 helix: 0.83 (0.26), residues: 426 sheet: -0.51 (0.36), residues: 186 loop : -0.57 (0.27), residues: 590 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.193 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 outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2176 time to fit residues: 64.1073 Evaluate side-chains 132 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 87 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11970 Z= 0.177 Angle : 0.594 7.731 16624 Z= 0.329 Chirality : 0.043 0.180 1790 Planarity : 0.005 0.043 1856 Dihedral : 22.696 136.734 2108 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.25), residues: 1202 helix: 0.90 (0.26), residues: 426 sheet: -0.59 (0.37), residues: 188 loop : -0.55 (0.28), residues: 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.243 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 outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.2059 time to fit residues: 61.7486 Evaluate side-chains 134 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 0.0020 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.0170 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 overall best weight: 0.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062503 restraints weight = 59967.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064389 restraints weight = 35530.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065684 restraints weight = 23585.478| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11970 Z= 0.175 Angle : 0.589 7.711 16624 Z= 0.325 Chirality : 0.043 0.190 1790 Planarity : 0.005 0.059 1856 Dihedral : 22.692 136.374 2108 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1202 helix: 0.87 (0.26), residues: 426 sheet: -0.55 (0.37), residues: 188 loop : -0.55 (0.28), residues: 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.85 seconds wall clock time: 44 minutes 46.47 seconds (2686.47 seconds total)