Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 04:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvm_14180/10_2023/7qvm_14180_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5450 2.51 5 N 1438 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R GLU 42": "OE1" <-> "OE2" Residue "R PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 189": "OD1" <-> "OD2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "L" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1994 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 239} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1770 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.02, per 1000 atoms: 0.59 Number of scatterers: 8528 At special positions: 0 Unit cell: (93.093, 122.388, 127.596, 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 65 16.00 O 1575 8.00 N 1438 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 33.3% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.754A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.024A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.551A pdb=" N ALA A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 36 through 64 removed outlier: 4.132A pdb=" N VAL R 60 " --> pdb=" O GLY R 56 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU R 61 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA R 63 " --> pdb=" O CYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.644A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 109 through 142 removed outlier: 3.858A pdb=" N THR R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 174 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 210 through 229 Processing helix chain 'R' and resid 271 through 300 Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 309 through 316 removed outlier: 3.795A pdb=" N LEU R 316 " --> pdb=" O ILE R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 332 Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 334 through 337 No H-bonds generated for 'chain 'R' and resid 334 through 337' 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 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' 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 264 through 270 removed outlier: 3.787A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 38 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 69 through 72 removed outlier: 5.905A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.797A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.158A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.697A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.885A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.778A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 4.107A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.420A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 7.224A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 386 hydrogen bonds defined for protein. 1104 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: 2.31 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 1455 1.46 - 1.58: 4547 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8709 Sorted by residual: bond pdb=" C THR S 84 " pdb=" N SER S 85 " ideal model delta sigma weight residual 1.333 1.266 0.066 1.29e-02 6.01e+03 2.65e+01 bond pdb=" N ILE L 3 " pdb=" CA ILE L 3 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.50e+00 bond pdb=" N GLN R 92 " pdb=" CA GLN R 92 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.24e-02 6.50e+03 7.27e+00 bond pdb=" N LEU R 316 " pdb=" CA LEU R 316 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.57e+00 bond pdb=" N GLN R 171 " pdb=" CA GLN R 171 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.45e+00 ... (remaining 8704 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.08: 123 105.08 - 112.32: 4465 112.32 - 119.56: 2817 119.56 - 126.79: 4276 126.79 - 134.03: 130 Bond angle restraints: 11811 Sorted by residual: angle pdb=" N TYR L 2 " pdb=" CA TYR L 2 " pdb=" C TYR L 2 " ideal model delta sigma weight residual 113.12 109.08 4.04 1.25e+00 6.40e-01 1.04e+01 angle pdb=" N ASP A 9 " pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 111.07 107.76 3.31 1.07e+00 8.73e-01 9.59e+00 angle pdb=" C THR S 84 " pdb=" N SER S 85 " pdb=" CA SER S 85 " ideal model delta sigma weight residual 122.63 127.03 -4.40 1.44e+00 4.82e-01 9.32e+00 angle pdb=" N MET A 249 " pdb=" CA MET A 249 " pdb=" C MET A 249 " ideal model delta sigma weight residual 110.97 107.66 3.31 1.09e+00 8.42e-01 9.24e+00 angle pdb=" CA LEU L 8 " pdb=" C LEU L 8 " pdb=" O LEU L 8 " ideal model delta sigma weight residual 121.20 118.17 3.03 1.04e+00 9.25e-01 8.50e+00 ... (remaining 11806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4698 17.96 - 35.92: 387 35.92 - 53.88: 55 53.88 - 71.84: 6 71.84 - 89.80: 6 Dihedral angle restraints: 5152 sinusoidal: 1980 harmonic: 3172 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -171.69 85.69 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 153.07 -60.07 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA GLN S 82 " pdb=" C GLN S 82 " pdb=" N MET S 83 " pdb=" CA MET S 83 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 895 0.035 - 0.070: 312 0.070 - 0.105: 94 0.105 - 0.140: 41 0.140 - 0.175: 9 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA GLU G 17 " pdb=" N GLU G 17 " pdb=" C GLU G 17 " pdb=" CB GLU G 17 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA MET A 249 " pdb=" N MET A 249 " pdb=" C MET A 249 " pdb=" CB MET A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA LEU A 250 " pdb=" N LEU A 250 " pdb=" C LEU A 250 " pdb=" CB LEU A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1348 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 341 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C ASP A 341 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 341 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 342 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.005 2.00e-02 2.50e+03 1.30e-02 4.24e+00 pdb=" CG TRP B 82 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.016 2.00e-02 2.50e+03 1.08e-02 2.92e+00 pdb=" CG TRP B 63 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.001 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 269 2.70 - 3.25: 8843 3.25 - 3.80: 13911 3.80 - 4.35: 17249 4.35 - 4.90: 29422 Nonbonded interactions: 69694 Sorted by model distance: nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.156 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.184 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.234 2.440 nonbonded pdb=" O ALA B 231 " pdb=" OG1 THR B 243 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.248 2.440 ... (remaining 69689 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 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 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: 0.010 Normalize map: mean=0, sd=1: 4.620 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: 14.690 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.060 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 0.066 8709 Z= 0.214 Angle : 0.640 6.556 11811 Z= 0.359 Chirality : 0.044 0.175 1351 Planarity : 0.004 0.043 1487 Dihedral : 12.937 89.801 3086 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1068 helix: 1.70 (0.29), residues: 353 sheet: -0.52 (0.32), residues: 241 loop : -0.63 (0.30), residues: 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2421 time to fit residues: 64.5029 Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2717 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8709 Z= 0.296 Angle : 0.614 6.116 11811 Z= 0.315 Chirality : 0.043 0.176 1351 Planarity : 0.004 0.043 1487 Dihedral : 4.374 23.076 1169 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.73 % Allowed : 11.87 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.31 (0.27), residues: 1068 helix: 2.17 (0.28), residues: 348 sheet: -0.78 (0.30), residues: 267 loop : -0.68 (0.31), residues: 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 0.2594 time to fit residues: 59.3960 Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0801 time to fit residues: 3.2090 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 307 GLN ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8709 Z= 0.245 Angle : 0.584 13.055 11811 Z= 0.296 Chirality : 0.042 0.186 1351 Planarity : 0.004 0.043 1487 Dihedral : 4.376 24.892 1169 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.76 % Allowed : 15.75 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.41 (0.27), residues: 1068 helix: 2.33 (0.28), residues: 347 sheet: -0.77 (0.30), residues: 267 loop : -0.64 (0.31), residues: 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 166 average time/residue: 0.2559 time to fit residues: 55.3101 Evaluate side-chains 151 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0695 time to fit residues: 1.5713 ------------------------------------------------------------------------------- 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: 7.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8709 Z= 0.198 Angle : 0.560 9.753 11811 Z= 0.285 Chirality : 0.042 0.181 1351 Planarity : 0.004 0.042 1487 Dihedral : 4.206 22.881 1169 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.62 % Allowed : 17.37 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.40 (0.27), residues: 1068 helix: 2.23 (0.27), residues: 359 sheet: -0.75 (0.30), residues: 276 loop : -0.65 (0.32), residues: 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 172 average time/residue: 0.2587 time to fit residues: 57.8850 Evaluate side-chains 162 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0815 time to fit residues: 2.2695 ------------------------------------------------------------------------------- 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: 7.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8709 Z= 0.226 Angle : 0.567 8.818 11811 Z= 0.290 Chirality : 0.041 0.184 1351 Planarity : 0.004 0.041 1487 Dihedral : 4.229 23.252 1169 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.19 % Allowed : 18.45 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.38 (0.27), residues: 1068 helix: 2.27 (0.27), residues: 357 sheet: -0.76 (0.30), residues: 277 loop : -0.71 (0.32), residues: 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 169 average time/residue: 0.2605 time to fit residues: 57.3132 Evaluate side-chains 162 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0868 time to fit residues: 2.2055 ------------------------------------------------------------------------------- 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: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 96 GLN S 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8709 Z= 0.348 Angle : 0.632 8.457 11811 Z= 0.324 Chirality : 0.043 0.201 1351 Planarity : 0.004 0.040 1487 Dihedral : 4.653 25.450 1169 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.62 % Allowed : 21.04 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.25 (0.27), residues: 1068 helix: 2.10 (0.27), residues: 361 sheet: -0.91 (0.29), residues: 287 loop : -0.68 (0.33), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 166 average time/residue: 0.2634 time to fit residues: 56.9277 Evaluate side-chains 158 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0870 time to fit residues: 2.3951 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.0040 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8709 Z= 0.182 Angle : 0.600 8.215 11811 Z= 0.301 Chirality : 0.042 0.208 1351 Planarity : 0.004 0.040 1487 Dihedral : 4.345 26.807 1169 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.97 % Allowed : 21.68 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1068 helix: 2.20 (0.27), residues: 360 sheet: -0.82 (0.30), residues: 271 loop : -0.64 (0.32), residues: 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 174 average time/residue: 0.2647 time to fit residues: 59.9199 Evaluate side-chains 159 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1017 time to fit residues: 2.1532 ------------------------------------------------------------------------------- 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: 0.1980 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8709 Z= 0.167 Angle : 0.600 9.453 11811 Z= 0.301 Chirality : 0.041 0.214 1351 Planarity : 0.004 0.040 1487 Dihedral : 4.200 28.012 1169 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.65 % Allowed : 22.22 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.50 (0.27), residues: 1068 helix: 2.12 (0.27), residues: 366 sheet: -0.51 (0.32), residues: 258 loop : -0.61 (0.31), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 169 average time/residue: 0.2625 time to fit residues: 57.6546 Evaluate side-chains 158 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0754 time to fit residues: 1.7967 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 0.0470 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8709 Z= 0.231 Angle : 0.627 9.700 11811 Z= 0.321 Chirality : 0.043 0.262 1351 Planarity : 0.004 0.045 1487 Dihedral : 4.320 29.217 1169 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.65 % Allowed : 22.87 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.41 (0.27), residues: 1068 helix: 2.16 (0.27), residues: 359 sheet: -0.68 (0.30), residues: 274 loop : -0.62 (0.32), residues: 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 155 average time/residue: 0.2820 time to fit residues: 56.3571 Evaluate side-chains 152 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1053 time to fit residues: 2.0680 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 66 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8709 Z= 0.173 Angle : 0.624 10.133 11811 Z= 0.314 Chirality : 0.042 0.249 1351 Planarity : 0.004 0.049 1487 Dihedral : 4.174 25.720 1169 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.43 % Allowed : 22.87 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.27), residues: 1068 helix: 2.11 (0.27), residues: 365 sheet: -0.51 (0.31), residues: 261 loop : -0.67 (0.31), residues: 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 160 average time/residue: 0.2747 time to fit residues: 56.4793 Evaluate side-chains 152 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0802 time to fit residues: 1.5264 ------------------------------------------------------------------------------- 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: 0.0870 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.122443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.088972 restraints weight = 16633.180| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.01 r_work: 0.3320 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8709 Z= 0.195 Angle : 0.638 11.024 11811 Z= 0.320 Chirality : 0.043 0.291 1351 Planarity : 0.004 0.050 1487 Dihedral : 4.204 24.856 1169 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.11 % Allowed : 23.95 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.27), residues: 1068 helix: 2.09 (0.27), residues: 365 sheet: -0.54 (0.31), residues: 251 loop : -0.65 (0.31), residues: 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.25 seconds wall clock time: 45 minutes 57.10 seconds (2757.10 seconds total)