Starting phenix.real_space_refine on Tue Jul 23 17:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/07_2024/8psz_17865_neut_trim.cif" } resolution = 2.42 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 56 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7221 2.51 5 N 2077 2.21 5 O 2481 1.98 5 H 11195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23098 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6653 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 bond proxies already assigned to first conformer: 7960 Chain: "C" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6652 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "S" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 411 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'A0I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.840 53.436 18.382 1.00 20.80 S ATOM 4474 SG CYS A 282 44.558 52.018 15.484 1.00 21.12 S ATOM 18191 SG CYS C 233 23.667 63.533 108.687 1.00 68.90 S ATOM 18215 SG CYS C 235 23.744 64.404 104.935 1.00 63.55 S ATOM 16857 SG CYS C 146 12.028 72.706 88.850 1.00 71.81 S ATOM 17045 SG CYS C 159 13.000 75.499 90.912 1.00 66.96 S ATOM 17101 SG CYS C 163 15.366 72.687 90.646 1.00 60.91 S ATOM 17111 SG CYS C 164 14.711 75.039 87.428 1.00 64.71 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP B 213 " occ=0.50 ... (22 atoms not shown) pdb=" HB3BASP B 213 " occ=0.50 residue: pdb=" N ATYR B 393 " occ=0.60 ... (40 atoms not shown) pdb=" HH BTYR B 393 " occ=0.40 Time building chain proxies: 14.61, per 1000 atoms: 0.63 Number of scatterers: 23098 At special positions: 0 Unit cell: (92.4, 109.2, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 56 15.00 Mg 2 11.99 O 2481 8.00 N 2077 7.00 C 7221 6.00 H 11195 1.00 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: 19.61 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 42.4% alpha, 13.9% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 11.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.878A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.523A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.967A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.555A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.501A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.648A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.646A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.728A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.972A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.035A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.736A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 removed outlier: 3.549A pdb=" N GLY C 165 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.627A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.540A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.302A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.302A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.129A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.779A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.623A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 20.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11163 1.03 - 1.23: 52 1.23 - 1.42: 5191 1.42 - 1.62: 6842 1.62 - 1.81: 89 Bond restraints: 23337 Sorted by residual: bond pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 1.731 1.618 0.113 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.30e-02 5.92e+03 1.98e+01 bond pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 1.701 1.641 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.662 1.603 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.691 1.642 0.049 2.00e-02 2.50e+03 5.88e+00 ... (remaining 23332 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 782 107.15 - 113.86: 27437 113.86 - 120.58: 7772 120.58 - 127.29: 5905 127.29 - 134.01: 227 Bond angle restraints: 42123 Sorted by residual: angle pdb=" O6 A0I B 601 " pdb=" P2 A0I B 601 " pdb=" O7 A0I B 601 " ideal model delta sigma weight residual 112.52 104.40 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" CB PRO C 234 " ideal model delta sigma weight residual 103.25 100.43 2.82 1.05e+00 9.07e-01 7.19e+00 angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.79e+00 angle pdb=" CA PRO C 234 " pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 120.60 116.81 3.79 1.82e+00 3.02e-01 4.33e+00 angle pdb=" N ASP C 345 " pdb=" CA ASP C 345 " pdb=" C ASP C 345 " ideal model delta sigma weight residual 114.75 112.49 2.26 1.26e+00 6.30e-01 3.22e+00 ... (remaining 42118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9721 17.80 - 35.60: 836 35.60 - 53.41: 342 53.41 - 71.21: 120 71.21 - 89.01: 29 Dihedral angle restraints: 11048 sinusoidal: 6454 harmonic: 4594 Sorted by residual: dihedral pdb=" CD ARG B 176 " pdb=" NE ARG B 176 " pdb=" CZ ARG B 176 " pdb=" NH1 ARG B 176 " ideal model delta sinusoidal sigma weight residual 0.00 41.02 -41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA SER B 286 " pdb=" C SER B 286 " pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1586 0.044 - 0.088: 227 0.088 - 0.132: 87 0.132 - 0.176: 0 0.176 - 0.220: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C7 A0I B 601 " pdb=" C6 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" O12 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.59 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL C 221 " pdb=" N VAL C 221 " pdb=" C VAL C 221 " pdb=" CB VAL C 221 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1898 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 176 " 0.749 9.50e-02 1.11e+02 2.50e-01 6.59e+01 pdb=" NE ARG B 176 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 176 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 176 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 176 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 176 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 176 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 176 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 176 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 3 " -0.022 2.00e-02 2.50e+03 9.08e-03 2.68e+00 pdb=" N9 A V 3 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 3 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 3 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 162 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.019 5.00e-02 4.00e+02 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 898 2.16 - 2.77: 43029 2.77 - 3.38: 65847 3.38 - 3.99: 89220 3.99 - 4.60: 135252 Nonbonded interactions: 334246 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.549 1.850 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.582 1.850 nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.590 1.850 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.630 1.850 nonbonded pdb=" HG1 THR B 103 " pdb=" O ILE B 125 " model vdw 1.631 1.850 ... (remaining 334241 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 'D' and resid 5 through 17) selection = (chain 'S' and (resid 28 through 34 or resid 36 through 40)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.340 Extract box with map and model: 0.800 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 95.000 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.113 12142 Z= 0.177 Angle : 0.493 8.121 16666 Z= 0.256 Chirality : 0.037 0.220 1901 Planarity : 0.008 0.321 1951 Dihedral : 17.754 89.008 4872 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.23), residues: 1351 helix: 1.65 (0.23), residues: 525 sheet: 0.20 (0.40), residues: 148 loop : -0.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 44 TYR 0.012 0.001 TYR C 315 ARG 0.007 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8594 (mttt) cc_final: 0.8364 (mttp) REVERT: A 332 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: B 282 ASP cc_start: 0.8477 (p0) cc_final: 0.8276 (p0) REVERT: B 480 GLU cc_start: 0.7593 (tt0) cc_final: 0.7385 (tt0) REVERT: C 77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (ptt90) REVERT: C 89 GLU cc_start: 0.7603 (mp0) cc_final: 0.7392 (mp0) REVERT: C 109 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mp10) REVERT: C 348 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7638 (mppt) REVERT: C 351 ILE cc_start: 0.7809 (mm) cc_final: 0.7532 (mm) REVERT: C 413 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7524 (mtmt) REVERT: C 427 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7088 (tttm) outliers start: 24 outliers final: 9 residues processed: 194 average time/residue: 3.6321 time to fit residues: 748.4986 Evaluate side-chains 128 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12142 Z= 0.358 Angle : 0.585 5.980 16666 Z= 0.311 Chirality : 0.041 0.140 1901 Planarity : 0.006 0.081 1951 Dihedral : 13.381 73.605 2316 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.32 % Allowed : 15.87 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.22), residues: 1351 helix: 1.57 (0.22), residues: 530 sheet: -0.08 (0.40), residues: 133 loop : -0.10 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 346 HIS 0.006 0.001 HIS A 371 PHE 0.018 0.002 PHE C 44 TYR 0.017 0.002 TYR A 403 ARG 0.005 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7525 (pptt) REVERT: C 109 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7043 (mp10) REVERT: C 348 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7683 (mppt) REVERT: C 351 ILE cc_start: 0.7781 (mm) cc_final: 0.7565 (mm) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 3.9439 time to fit residues: 621.7349 Evaluate side-chains 133 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12142 Z= 0.183 Angle : 0.496 5.507 16666 Z= 0.261 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.936 73.616 2308 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.54 % Allowed : 16.81 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.22), residues: 1351 helix: 1.85 (0.23), residues: 523 sheet: -0.07 (0.41), residues: 133 loop : -0.08 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8202 (pptt) cc_final: 0.7990 (pttm) REVERT: B 53 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7444 (pptt) REVERT: C 109 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7137 (mp10) REVERT: C 196 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6218 (mt-10) REVERT: C 348 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7614 (mppt) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 3.9699 time to fit residues: 571.4915 Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12142 Z= 0.202 Angle : 0.496 5.622 16666 Z= 0.261 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.061 1951 Dihedral : 12.840 73.596 2307 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.89 % Allowed : 15.87 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1351 helix: 1.91 (0.23), residues: 523 sheet: -0.14 (0.41), residues: 133 loop : -0.07 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7354 (pptt) REVERT: C 109 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7137 (mp10) REVERT: C 196 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6195 (mt-10) REVERT: C 348 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7622 (mppt) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 3.6745 time to fit residues: 530.9296 Evaluate side-chains 131 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12142 Z= 0.315 Angle : 0.551 6.138 16666 Z= 0.291 Chirality : 0.039 0.140 1901 Planarity : 0.005 0.060 1951 Dihedral : 12.942 73.531 2303 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.89 % Allowed : 16.12 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.22), residues: 1351 helix: 1.69 (0.22), residues: 523 sheet: -0.22 (0.41), residues: 133 loop : -0.18 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.016 0.002 PHE C 44 TYR 0.016 0.002 TYR A 403 ARG 0.004 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7511 (pptt) REVERT: C 109 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7160 (mp10) REVERT: C 196 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6193 (mt-10) REVERT: C 348 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7737 (mppt) REVERT: C 352 LYS cc_start: 0.7911 (mptt) cc_final: 0.7462 (mtpp) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 3.6387 time to fit residues: 519.2144 Evaluate side-chains 136 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 390 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12142 Z= 0.191 Angle : 0.491 5.773 16666 Z= 0.258 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.060 1951 Dihedral : 12.770 73.562 2303 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.20 % Allowed : 16.72 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.22), residues: 1351 helix: 1.89 (0.23), residues: 523 sheet: -0.14 (0.41), residues: 133 loop : -0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7173 (mp10) REVERT: C 196 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6190 (mt-10) REVERT: C 348 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7697 (mppt) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 3.9518 time to fit residues: 514.8490 Evaluate side-chains 123 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12142 Z= 0.148 Angle : 0.466 5.628 16666 Z= 0.244 Chirality : 0.036 0.138 1901 Planarity : 0.004 0.053 1951 Dihedral : 12.605 73.555 2302 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.46 % Allowed : 16.47 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1351 helix: 2.06 (0.23), residues: 524 sheet: 0.01 (0.41), residues: 133 loop : -0.01 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 161 TYR 0.011 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8850 (mt) REVERT: C 109 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7147 (mp10) REVERT: C 348 LYS cc_start: 0.7927 (mmtp) cc_final: 0.7675 (mppt) outliers start: 17 outliers final: 11 residues processed: 132 average time/residue: 3.7574 time to fit residues: 526.5962 Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12142 Z= 0.231 Angle : 0.505 5.697 16666 Z= 0.266 Chirality : 0.037 0.136 1901 Planarity : 0.004 0.077 1951 Dihedral : 12.711 73.591 2302 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.46 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1351 helix: 1.92 (0.23), residues: 524 sheet: -0.09 (0.41), residues: 133 loop : -0.07 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.006 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.631 Fit side-chains REVERT: B 159 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8846 (mt) REVERT: C 109 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7133 (mp10) outliers start: 17 outliers final: 14 residues processed: 128 average time/residue: 3.8693 time to fit residues: 524.8328 Evaluate side-chains 126 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12142 Z= 0.173 Angle : 0.482 5.547 16666 Z= 0.252 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.074 1951 Dihedral : 12.622 73.561 2302 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.20 % Allowed : 16.64 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1351 helix: 2.03 (0.23), residues: 524 sheet: -0.05 (0.41), residues: 133 loop : -0.03 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.868 Fit side-chains REVERT: B 159 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8841 (mt) REVERT: C 28 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5826 (t-90) REVERT: C 109 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7134 (mp10) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 3.8409 time to fit residues: 509.5416 Evaluate side-chains 125 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12142 Z= 0.157 Angle : 0.474 5.327 16666 Z= 0.247 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.077 1951 Dihedral : 12.541 73.548 2302 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.11 % Allowed : 16.81 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.23), residues: 1351 helix: 2.10 (0.23), residues: 524 sheet: 0.01 (0.41), residues: 133 loop : 0.01 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.011 0.001 TYR A 403 ARG 0.009 0.000 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.856 Fit side-chains REVERT: B 159 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8855 (mt) REVERT: C 109 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7086 (mp10) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 3.7045 time to fit residues: 492.1930 Evaluate side-chains 126 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.086114 restraints weight = 52553.378| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.77 r_work: 0.2814 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12142 Z= 0.159 Angle : 0.475 5.274 16666 Z= 0.248 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.076 1951 Dihedral : 12.495 73.543 2301 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 16.98 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1351 helix: 2.12 (0.23), residues: 524 sheet: 0.04 (0.42), residues: 133 loop : 0.01 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.011 0.001 TYR A 403 ARG 0.013 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10074.87 seconds wall clock time: 174 minutes 1.59 seconds (10441.59 seconds total)