Starting phenix.real_space_refine (version: dev) on Sat Feb 18 16:56:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2023/7y12_33554_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 275": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8501 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1654 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'BAL': 1, 'PLM': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.30, per 1000 atoms: 0.62 Number of scatterers: 8501 At special positions: 0 Unit cell: (122.85, 84.375, 124.2, 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 69 16.00 O 1547 8.00 N 1454 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 2082 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.807A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.075A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.887A pdb=" N VAL A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 63 through 87 Processing helix chain 'R' and resid 93 through 128 removed outlier: 3.985A pdb=" N VAL R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 141 through 162 Processing helix chain 'R' and resid 172 through 208 removed outlier: 5.168A pdb=" N THR R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 217 through 233 Processing helix chain 'R' and resid 235 through 246 removed outlier: 5.040A pdb=" N TYR R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP R 246 " --> pdb=" O PHE R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 276 Proline residue: R 273 - end of helix Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.173A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.034A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.401A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.958A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.596A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.764A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.508A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1083 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: 2.36 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2292 1.33 - 1.45: 1585 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8676 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.306 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.508 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.512 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C LEU R 235 " pdb=" N PRO R 236 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.65: 197 106.65 - 113.48: 4837 113.48 - 120.31: 3002 120.31 - 127.14: 3624 127.14 - 133.98: 96 Bond angle restraints: 11756 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.33 7.47 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CB MET R 42 " pdb=" CG MET R 42 " pdb=" SD MET R 42 " ideal model delta sigma weight residual 112.70 123.74 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MET R 42 " pdb=" CB MET R 42 " pdb=" CG MET R 42 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.25e+00 angle pdb=" N MET R 42 " pdb=" CA MET R 42 " pdb=" CB MET R 42 " ideal model delta sigma weight residual 110.30 114.67 -4.37 1.54e+00 4.22e-01 8.03e+00 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4517 17.97 - 35.93: 479 35.93 - 53.90: 110 53.90 - 71.86: 13 71.86 - 89.83: 12 Dihedral angle restraints: 5131 sinusoidal: 1912 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.90 29.10 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP B 303 " pdb=" CB ASP B 303 " pdb=" CG ASP B 303 " pdb=" OD1 ASP B 303 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 808 0.028 - 0.056: 355 0.056 - 0.085: 112 0.085 - 0.113: 67 0.113 - 0.141: 15 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1354 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.010 2.00e-02 2.50e+03 9.66e-03 1.87e+00 pdb=" CG TYR B 105 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 236 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 240 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C TYR R 240 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR R 240 " -0.008 2.00e-02 2.50e+03 pdb=" N TRP R 241 " -0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 131 2.65 - 3.21: 7668 3.21 - 3.77: 13416 3.77 - 4.34: 18426 4.34 - 4.90: 30789 Nonbonded interactions: 70430 Sorted by model distance: nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.086 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.147 2.440 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASN A 241 " pdb=" OH TYR A 287 " model vdw 2.213 2.440 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.262 2.440 ... (remaining 70425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5431 2.51 5 N 1454 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.860 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: 7.760 Check model and map are aligned: 0.130 Process input model: 25.400 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.003 0.059 8676 Z= 0.222 Angle : 0.581 11.036 11756 Z= 0.295 Chirality : 0.040 0.141 1357 Planarity : 0.003 0.033 1468 Dihedral : 15.813 89.828 3043 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.27), residues: 1093 helix: 2.18 (0.28), residues: 361 sheet: -0.05 (0.32), residues: 271 loop : -0.27 (0.30), residues: 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.007 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2232 time to fit residues: 44.3436 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0911 time to fit residues: 1.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.0040 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.134 Angle : 0.468 5.459 11756 Z= 0.253 Chirality : 0.039 0.144 1357 Planarity : 0.003 0.034 1468 Dihedral : 5.285 50.436 1238 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.02 (0.27), residues: 1093 helix: 2.35 (0.28), residues: 365 sheet: -0.01 (0.32), residues: 271 loop : -0.21 (0.31), residues: 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.036 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 161 average time/residue: 0.2176 time to fit residues: 48.4861 Evaluate side-chains 156 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0882 time to fit residues: 3.1945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8676 Z= 0.287 Angle : 0.560 6.987 11756 Z= 0.299 Chirality : 0.042 0.156 1357 Planarity : 0.004 0.033 1468 Dihedral : 6.070 59.974 1238 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.65 (0.26), residues: 1093 helix: 1.98 (0.28), residues: 356 sheet: -0.13 (0.31), residues: 287 loop : -0.37 (0.30), residues: 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.010 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.2171 time to fit residues: 44.4365 Evaluate side-chains 147 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0811 time to fit residues: 2.4696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.157 Angle : 0.482 5.575 11756 Z= 0.258 Chirality : 0.039 0.145 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.318 54.169 1238 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.87 (0.27), residues: 1093 helix: 2.17 (0.28), residues: 362 sheet: -0.07 (0.32), residues: 275 loop : -0.23 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.000 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 149 average time/residue: 0.2070 time to fit residues: 42.9648 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0892 time to fit residues: 2.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.181 Angle : 0.503 9.645 11756 Z= 0.263 Chirality : 0.039 0.144 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.326 56.762 1238 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.87 (0.26), residues: 1093 helix: 2.16 (0.28), residues: 362 sheet: -0.06 (0.31), residues: 275 loop : -0.24 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.079 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 154 average time/residue: 0.2140 time to fit residues: 45.9120 Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0850 time to fit residues: 2.5790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8676 Z= 0.161 Angle : 0.491 8.802 11756 Z= 0.258 Chirality : 0.039 0.143 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.145 57.166 1238 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.96 (0.27), residues: 1093 helix: 2.21 (0.28), residues: 369 sheet: -0.04 (0.32), residues: 275 loop : -0.16 (0.31), residues: 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.976 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 154 average time/residue: 0.2101 time to fit residues: 45.0012 Evaluate side-chains 149 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0867 time to fit residues: 2.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8676 Z= 0.189 Angle : 0.513 8.227 11756 Z= 0.269 Chirality : 0.040 0.157 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.287 59.925 1238 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.26), residues: 1093 helix: 2.19 (0.28), residues: 356 sheet: -0.07 (0.31), residues: 275 loop : -0.32 (0.30), residues: 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.026 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 154 average time/residue: 0.2245 time to fit residues: 48.3046 Evaluate side-chains 150 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0793 time to fit residues: 2.1676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.198 Angle : 0.514 7.953 11756 Z= 0.271 Chirality : 0.040 0.146 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.352 57.408 1238 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1093 helix: 2.18 (0.28), residues: 356 sheet: -0.07 (0.31), residues: 275 loop : -0.34 (0.30), residues: 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 0.946 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 146 average time/residue: 0.2201 time to fit residues: 44.0672 Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1429 time to fit residues: 2.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.169 Angle : 0.514 7.734 11756 Z= 0.269 Chirality : 0.040 0.191 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.164 57.181 1238 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.87 (0.26), residues: 1093 helix: 2.16 (0.28), residues: 363 sheet: -0.05 (0.32), residues: 275 loop : -0.25 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.018 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.2301 time to fit residues: 46.0661 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0845 time to fit residues: 1.5845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.002 0.034 8676 Z= 0.154 Angle : 0.500 7.569 11756 Z= 0.262 Chirality : 0.039 0.169 1357 Planarity : 0.003 0.033 1468 Dihedral : 4.984 56.080 1238 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.94 (0.27), residues: 1093 helix: 2.19 (0.28), residues: 370 sheet: -0.07 (0.31), residues: 277 loop : -0.18 (0.31), residues: 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.087 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 0.2364 time to fit residues: 46.4981 Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0853 time to fit residues: 1.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.170026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136161 restraints weight = 10325.466| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.04 r_work: 0.3423 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.216 Angle : 0.534 7.417 11756 Z= 0.281 Chirality : 0.041 0.169 1357 Planarity : 0.003 0.032 1468 Dihedral : 5.413 54.862 1238 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.76 (0.26), residues: 1093 helix: 2.12 (0.28), residues: 357 sheet: -0.07 (0.31), residues: 277 loop : -0.35 (0.30), residues: 459 =============================================================================== Job complete usr+sys time: 2054.17 seconds wall clock time: 38 minutes 29.96 seconds (2309.96 seconds total)