Starting phenix.real_space_refine on Fri Nov 17 02:36:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/11_2023/6voy_21301.pdb" } resolution = 3.7 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= 0.002 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 178 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 10706 2.51 5 N 3072 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "J" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 246 SG CYS A 33 63.285 78.778 64.823 1.00116.78 S ATOM 267 SG CYS A 36 64.894 75.597 65.874 1.00 99.36 S ATOM 2439 SG CYS B 33 137.488 80.123 80.291 1.00299.42 S ATOM 2460 SG CYS B 36 138.441 77.611 78.802 1.00269.90 S ATOM 4504 SG CYS C 33 105.877 38.294 66.337 1.00107.32 S ATOM 4525 SG CYS C 36 104.269 41.389 64.821 1.00 95.45 S ATOM 6697 SG CYS D 33 31.902 36.894 81.648 1.00337.40 S ATOM 6718 SG CYS D 36 30.371 38.588 79.947 1.00308.22 S Time building chain proxies: 9.70, per 1000 atoms: 0.55 Number of scatterers: 17556 At special positions: 0 Unit cell: (170.62, 115.236, 139.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 54 16.00 P 178 15.00 Mg 2 11.99 O 3540 8.00 N 3072 7.00 C 10706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 10 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 6 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 10 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 6 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 36 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 6 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 10 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 36 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 10 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 6 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 36 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 33 " Number of angles added : 7 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 51.7% alpha, 4.1% beta 82 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 7.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 171 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 152 through 172 Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 171 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 63 through 83 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 175 through 193 Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 221 through 234 Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 277 through 286 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 298 through 310 Processing helix chain 'E' and resid 320 through 332 removed outlier: 4.731A pdb=" N GLU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) Proline residue: E 326 - end of helix removed outlier: 3.696A pdb=" N GLN E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 83 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 Processing helix chain 'F' and resid 194 through 213 Processing helix chain 'F' and resid 221 through 234 Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 277 through 286 Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 298 through 310 Processing helix chain 'F' and resid 320 through 332 removed outlier: 4.702A pdb=" N GLU F 325 " --> pdb=" O VAL F 321 " (cutoff:3.500A) Proline residue: F 326 - end of helix removed outlier: 3.701A pdb=" N GLN F 330 " --> pdb=" O PRO F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 353 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.195A pdb=" N GLN B 244 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 230 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY B 242 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 117 589 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3018 1.32 - 1.45: 5935 1.45 - 1.58: 9006 1.58 - 1.70: 347 1.70 - 1.83: 80 Bond restraints: 18386 Sorted by residual: bond pdb=" CG PRO D 243 " pdb=" CD PRO D 243 " ideal model delta sigma weight residual 1.503 1.348 0.155 3.40e-02 8.65e+02 2.09e+01 bond pdb=" CB TRP A 240 " pdb=" CG TRP A 240 " ideal model delta sigma weight residual 1.498 1.362 0.136 3.10e-02 1.04e+03 1.94e+01 bond pdb=" CB TRP C 60 " pdb=" CG TRP C 60 " ideal model delta sigma weight residual 1.498 1.368 0.130 3.10e-02 1.04e+03 1.76e+01 bond pdb=" CB ASN B 118 " pdb=" CG ASN B 118 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.52e+01 bond pdb=" CB TRP C 240 " pdb=" CG TRP C 240 " ideal model delta sigma weight residual 1.498 1.388 0.110 3.10e-02 1.04e+03 1.25e+01 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 78.86 - 93.21: 2 93.21 - 107.56: 2489 107.56 - 121.91: 19516 121.91 - 136.26: 3760 136.26 - 150.62: 1 Bond angle restraints: 25768 Sorted by residual: angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 110.63 78.86 31.77 1.94e+00 2.66e-01 2.68e+02 angle pdb=" C TRP D 227 " pdb=" N TYR D 228 " pdb=" CA TYR D 228 " ideal model delta sigma weight residual 121.70 150.62 -28.92 1.80e+00 3.09e-01 2.58e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" C PHE C 230 " ideal model delta sigma weight residual 112.12 132.09 -19.97 1.34e+00 5.57e-01 2.22e+02 angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" C PHE A 230 " ideal model delta sigma weight residual 112.12 131.73 -19.61 1.34e+00 5.57e-01 2.14e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 110.63 83.38 27.25 1.94e+00 2.66e-01 1.97e+02 ... (remaining 25763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9265 35.22 - 70.43: 963 70.43 - 105.65: 52 105.65 - 140.86: 5 140.86 - 176.08: 9 Dihedral angle restraints: 10294 sinusoidal: 5190 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLU E 276 " pdb=" C GLU E 276 " pdb=" N LYS E 277 " pdb=" CA LYS E 277 " ideal model delta harmonic sigma weight residual -180.00 -49.46 -130.54 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLU F 276 " pdb=" C GLU F 276 " pdb=" N LYS F 277 " pdb=" CA LYS F 277 " ideal model delta harmonic sigma weight residual -180.00 -50.02 -129.98 0 5.00e+00 4.00e-02 6.76e+02 dihedral pdb=" CA GLN A 244 " pdb=" C GLN A 244 " pdb=" N GLU A 245 " pdb=" CA GLU A 245 " ideal model delta harmonic sigma weight residual -180.00 -83.94 -96.06 0 5.00e+00 4.00e-02 3.69e+02 ... (remaining 10291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2853 0.336 - 0.672: 23 0.672 - 1.009: 4 1.009 - 1.345: 1 1.345 - 1.681: 1 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR D 228 " pdb=" N TYR D 228 " pdb=" C TYR D 228 " pdb=" CB TYR D 228 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" CA PRO C 243 " pdb=" N PRO C 243 " pdb=" C PRO C 243 " pdb=" CB PRO C 243 " both_signs ideal model delta sigma weight residual False 2.72 1.71 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO A 243 " pdb=" N PRO A 243 " pdb=" C PRO A 243 " pdb=" CB PRO A 243 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2879 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 153 " 0.043 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C GLY B 153 " -0.149 2.00e-02 2.50e+03 pdb=" O GLY B 153 " 0.056 2.00e-02 2.50e+03 pdb=" N LEU B 154 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 132 " -0.041 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C PRO F 132 " 0.138 2.00e-02 2.50e+03 pdb=" O PRO F 132 " -0.051 2.00e-02 2.50e+03 pdb=" N HIS F 133 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 132 " 0.041 2.00e-02 2.50e+03 8.00e-02 6.39e+01 pdb=" C PRO E 132 " -0.138 2.00e-02 2.50e+03 pdb=" O PRO E 132 " 0.051 2.00e-02 2.50e+03 pdb=" N HIS E 133 " 0.047 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 47 2.25 - 2.91: 8538 2.91 - 3.57: 28016 3.57 - 4.24: 42570 4.24 - 4.90: 62808 Nonbonded interactions: 141979 Sorted by model distance: nonbonded pdb=" O TRP A 60 " pdb=" O VAL A 80 " model vdw 1.583 3.040 nonbonded pdb=" CD2 HIS B 6 " pdb=" CD2 HIS B 10 " model vdw 1.769 3.480 nonbonded pdb=" O GLY C 122 " pdb=" N TYR C 125 " model vdw 1.971 2.520 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 302 " model vdw 1.992 2.170 nonbonded pdb=" NE2 GLN A 44 " pdb=" OP1 DT J 10 " model vdw 2.005 2.520 ... (remaining 141974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'B' and resid 1 through 274) selection = (chain 'C' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'D' and resid 1 through 274) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.020 Extract box with map and model: 5.040 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 58.650 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.013 0.155 18386 Z= 0.778 Angle : 1.522 31.766 25768 Z= 0.887 Chirality : 0.100 1.681 2882 Planarity : 0.013 0.095 2630 Dihedral : 24.389 176.075 6970 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 35.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.46 % Allowed : 13.41 % Favored : 86.12 % Cbeta Deviations : 1.81 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.96 % Twisted General : 1.49 % 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: -6.32 (0.14), residues: 1700 helix: -4.02 (0.11), residues: 784 sheet: -3.45 (0.47), residues: 100 loop : -4.53 (0.16), residues: 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 433 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 437 average time/residue: 0.3225 time to fit residues: 204.4072 Evaluate side-chains 363 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 165 optimal weight: 0.0010 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 132 ASN A 141 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 204 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 226 HIS A 236 ASN B 34 HIS B 141 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 236 ASN D 61 GLN D 77 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 133 HIS E 187 HIS E 205 ASN E 233 ASN E 306 ASN E 330 GLN F 48 GLN F 85 ASN F 187 HIS F 205 ASN F 233 ASN F 306 ASN F 330 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 18386 Z= 0.421 Angle : 0.974 17.300 25768 Z= 0.525 Chirality : 0.053 0.463 2882 Planarity : 0.007 0.074 2630 Dihedral : 28.338 176.359 3640 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.59 % Allowed : 16.65 % Favored : 82.76 % Rotamer: Outliers : 3.85 % Allowed : 22.97 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.93 % 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: -4.44 (0.18), residues: 1700 helix: -2.13 (0.15), residues: 768 sheet: -2.95 (0.44), residues: 110 loop : -3.84 (0.20), residues: 822 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 412 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 42 residues processed: 436 average time/residue: 0.2915 time to fit residues: 193.1595 Evaluate side-chains 419 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 377 time to evaluate : 1.796 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.1561 time to fit residues: 14.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.0370 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 164 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18386 Z= 0.265 Angle : 0.867 15.126 25768 Z= 0.465 Chirality : 0.049 0.393 2882 Planarity : 0.005 0.050 2630 Dihedral : 28.067 177.196 3640 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.41 % Favored : 88.12 % Rotamer: Outliers : 4.18 % Allowed : 24.10 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.45 (0.19), residues: 1700 helix: -1.03 (0.18), residues: 768 sheet: -2.86 (0.40), residues: 128 loop : -3.57 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 414 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 444 average time/residue: 0.2828 time to fit residues: 189.1369 Evaluate side-chains 418 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 388 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1884 time to fit residues: 11.9668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18386 Z= 0.323 Angle : 0.874 15.081 25768 Z= 0.468 Chirality : 0.050 0.372 2882 Planarity : 0.005 0.044 2630 Dihedral : 27.950 177.820 3640 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.88 % Favored : 85.65 % Rotamer: Outliers : 4.65 % Allowed : 27.36 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -3.36 (0.19), residues: 1700 helix: -0.92 (0.18), residues: 796 sheet: -2.31 (0.46), residues: 108 loop : -3.72 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 385 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 31 residues processed: 418 average time/residue: 0.3036 time to fit residues: 192.7612 Evaluate side-chains 399 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 368 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1654 time to fit residues: 11.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.0050 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 132 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN E 264 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18386 Z= 0.245 Angle : 0.850 13.813 25768 Z= 0.448 Chirality : 0.049 0.376 2882 Planarity : 0.005 0.055 2630 Dihedral : 27.793 177.490 3640 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.06 % Favored : 87.65 % Rotamer: Outliers : 2.99 % Allowed : 28.49 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -3.00 (0.19), residues: 1700 helix: -0.63 (0.18), residues: 782 sheet: -1.64 (0.52), residues: 92 loop : -3.55 (0.20), residues: 826 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 410 time to evaluate : 1.850 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 15 residues processed: 432 average time/residue: 0.2833 time to fit residues: 184.3917 Evaluate side-chains 386 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 371 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1398 time to fit residues: 6.0225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 0.0270 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN F 38 GLN F 233 ASN F 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18386 Z= 0.237 Angle : 0.866 13.794 25768 Z= 0.453 Chirality : 0.050 0.430 2882 Planarity : 0.005 0.052 2630 Dihedral : 27.634 177.504 3640 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.65 % Favored : 87.06 % Rotamer: Outliers : 2.92 % Allowed : 30.01 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -2.90 (0.20), residues: 1700 helix: -0.55 (0.18), residues: 782 sheet: -2.00 (0.45), residues: 112 loop : -3.44 (0.20), residues: 806 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 398 time to evaluate : 1.915 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 417 average time/residue: 0.3001 time to fit residues: 186.9195 Evaluate side-chains 406 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 381 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1599 time to fit residues: 9.6213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 GLN A 91 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS E 233 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18386 Z= 0.290 Angle : 0.875 12.967 25768 Z= 0.459 Chirality : 0.050 0.453 2882 Planarity : 0.005 0.047 2630 Dihedral : 27.583 177.863 3640 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.53 % Favored : 86.24 % Rotamer: Outliers : 2.32 % Allowed : 31.74 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.90 (0.20), residues: 1700 helix: -0.58 (0.18), residues: 782 sheet: -1.91 (0.46), residues: 112 loop : -3.43 (0.20), residues: 806 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 389 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 410 average time/residue: 0.2916 time to fit residues: 180.2245 Evaluate side-chains 386 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 366 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1658 time to fit residues: 8.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN E 233 ASN F 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18386 Z= 0.238 Angle : 0.878 16.530 25768 Z= 0.455 Chirality : 0.050 0.410 2882 Planarity : 0.005 0.055 2630 Dihedral : 27.431 176.877 3640 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.06 % Favored : 87.71 % Rotamer: Outliers : 1.39 % Allowed : 31.81 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.74 (0.20), residues: 1700 helix: -0.43 (0.19), residues: 760 sheet: -1.84 (0.44), residues: 112 loop : -3.29 (0.21), residues: 828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 415 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 423 average time/residue: 0.3064 time to fit residues: 192.7129 Evaluate side-chains 401 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 390 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1639 time to fit residues: 5.6497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN F 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18386 Z= 0.249 Angle : 0.885 15.654 25768 Z= 0.458 Chirality : 0.050 0.428 2882 Planarity : 0.005 0.059 2630 Dihedral : 27.356 177.248 3640 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.65 % Favored : 87.12 % Rotamer: Outliers : 1.06 % Allowed : 32.87 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.76 (0.20), residues: 1700 helix: -0.51 (0.19), residues: 778 sheet: -1.56 (0.46), residues: 108 loop : -3.33 (0.21), residues: 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 411 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 417 average time/residue: 0.2953 time to fit residues: 184.7684 Evaluate side-chains 400 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 393 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1556 time to fit residues: 4.4086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0970 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 144 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 233 ASN F 187 HIS F 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18386 Z= 0.252 Angle : 0.902 15.518 25768 Z= 0.463 Chirality : 0.050 0.428 2882 Planarity : 0.005 0.057 2630 Dihedral : 27.281 177.141 3640 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.18 % Favored : 87.59 % Rotamer: Outliers : 0.53 % Allowed : 33.93 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.74 (0.20), residues: 1700 helix: -0.53 (0.18), residues: 778 sheet: -1.63 (0.46), residues: 108 loop : -3.26 (0.21), residues: 814 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 408 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 410 average time/residue: 0.2851 time to fit residues: 175.8677 Evaluate side-chains 397 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 393 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1665 time to fit residues: 3.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.0970 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.0070 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN F 187 HIS F 233 ASN F 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.184835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131512 restraints weight = 37877.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135295 restraints weight = 16917.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137612 restraints weight = 10766.795| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18386 Z= 0.236 Angle : 0.903 16.981 25768 Z= 0.462 Chirality : 0.050 0.425 2882 Planarity : 0.005 0.061 2630 Dihedral : 27.155 177.084 3640 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.18 % Favored : 87.76 % Rotamer: Outliers : 0.33 % Allowed : 34.40 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.69 (0.20), residues: 1700 helix: -0.54 (0.18), residues: 780 sheet: -1.50 (0.46), residues: 108 loop : -3.20 (0.21), residues: 812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4177.00 seconds wall clock time: 76 minutes 55.93 seconds (4615.93 seconds total)