Starting phenix.real_space_refine (version: dev) on Sat Feb 18 20:02:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0q_22608/02_2023/7k0q_22608_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8778 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1159 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 134} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLP': 1, 'VRP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.63 Number of scatterers: 8778 At special positions: 0 Unit cell: (89.445, 87.435, 119.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 1597 8.00 N 1484 7.00 C 5647 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 5 sheets defined 47.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.516A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.497A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.882A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.833A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.548A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 434 through 456 removed outlier: 3.809A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 4.111A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 55 removed outlier: 4.063A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 18 removed outlier: 4.750A pdb=" N MET D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 79 through 82 removed outlier: 4.507A pdb=" N LEU D 82 " --> pdb=" O LYS D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 85 through 92 removed outlier: 5.909A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.860A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing sheet with id= A, first strand: chain 'A' and resid 93 through 95 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.714A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= D, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.503A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 468 through 472 377 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2784 1.34 - 1.46: 1345 1.46 - 1.57: 4755 1.57 - 1.69: 3 1.69 - 1.81: 81 Bond restraints: 8968 Sorted by residual: bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 7.00e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.13e+00 bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.00e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.73e+00 bond pdb=" C18 VRP B 602 " pdb=" C19 VRP B 602 " ideal model delta sigma weight residual 1.538 1.578 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 8963 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 253 106.47 - 113.35: 4900 113.35 - 120.24: 3376 120.24 - 127.12: 3517 127.12 - 134.00: 89 Bond angle restraints: 12135 Sorted by residual: angle pdb=" CA GLY B 385 " pdb=" C GLY B 385 " pdb=" N GLY B 386 " ideal model delta sigma weight residual 114.23 117.30 -3.07 8.80e-01 1.29e+00 1.22e+01 angle pdb=" C TYR B 474 " pdb=" N MET B 475 " pdb=" CA MET B 475 " ideal model delta sigma weight residual 122.74 114.47 8.27 2.44e+00 1.68e-01 1.15e+01 angle pdb=" C ARG A 422 " pdb=" N SER A 423 " pdb=" CA SER A 423 " ideal model delta sigma weight residual 122.74 127.52 -4.78 1.44e+00 4.82e-01 1.10e+01 angle pdb=" N TYR B 474 " pdb=" CA TYR B 474 " pdb=" CB TYR B 474 " ideal model delta sigma weight residual 114.17 110.70 3.47 1.14e+00 7.69e-01 9.26e+00 angle pdb=" N ASN D 151 " pdb=" CA ASN D 151 " pdb=" C ASN D 151 " ideal model delta sigma weight residual 112.86 109.15 3.71 1.22e+00 6.72e-01 9.23e+00 ... (remaining 12130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4936 17.94 - 35.89: 355 35.89 - 53.83: 56 53.83 - 71.77: 12 71.77 - 89.72: 3 Dihedral angle restraints: 5362 sinusoidal: 2159 harmonic: 3203 Sorted by residual: dihedral pdb=" CA ARG B 105 " pdb=" C ARG B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" N ARG B 507 " pdb=" CA ARG B 507 " ideal model delta harmonic sigma weight residual 180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR B 115 " pdb=" C TYR B 115 " pdb=" N GLN B 116 " pdb=" CA GLN B 116 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 936 0.043 - 0.085: 309 0.085 - 0.128: 90 0.128 - 0.171: 15 0.171 - 0.214: 2 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 1349 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO B 413 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 470 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 58 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 58 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 58 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 58 " 0.010 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 119 2.67 - 3.23: 8380 3.23 - 3.79: 12888 3.79 - 4.34: 17566 4.34 - 4.90: 30284 Nonbonded interactions: 69237 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.116 2.440 nonbonded pdb=" NH2 ARG B 105 " pdb=" OE2 GLU B 107 " model vdw 2.227 2.520 nonbonded pdb=" NH2 ARG A 422 " pdb=" OE1 GLU A 466 " model vdw 2.255 2.520 nonbonded pdb=" O ARG A 422 " pdb=" OG SER A 423 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR D 74 " pdb=" OD1 ASP D 76 " model vdw 2.268 2.440 ... (remaining 69232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5647 2.51 5 N 1484 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.000 Check model and map are aligned: 0.140 Process input model: 26.030 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.006 0.048 8968 Z= 0.426 Angle : 0.700 8.754 12135 Z= 0.411 Chirality : 0.047 0.214 1352 Planarity : 0.004 0.061 1544 Dihedral : 12.642 89.718 3314 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.00 % 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: 0.45 (0.25), residues: 1099 helix: 1.43 (0.23), residues: 537 sheet: -0.30 (0.44), residues: 124 loop : -0.91 (0.27), residues: 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2098 time to fit residues: 34.8075 Evaluate side-chains 98 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 51 optimal weight: 0.0470 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.0170 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8968 Z= 0.157 Angle : 0.471 6.698 12135 Z= 0.252 Chirality : 0.042 0.193 1352 Planarity : 0.004 0.050 1544 Dihedral : 4.638 45.044 1229 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.96 % 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: 0.93 (0.25), residues: 1099 helix: 1.87 (0.23), residues: 535 sheet: -0.17 (0.44), residues: 124 loop : -0.70 (0.27), residues: 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.121 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 113 average time/residue: 0.2171 time to fit residues: 34.7201 Evaluate side-chains 108 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0886 time to fit residues: 2.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 67 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.0970 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 116 GLN D 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8968 Z= 0.141 Angle : 0.433 6.674 12135 Z= 0.230 Chirality : 0.041 0.190 1352 Planarity : 0.003 0.045 1544 Dihedral : 4.221 45.966 1229 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.75 % 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: 1.14 (0.25), residues: 1099 helix: 2.06 (0.23), residues: 539 sheet: -0.06 (0.45), residues: 124 loop : -0.65 (0.27), residues: 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.022 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 114 average time/residue: 0.2246 time to fit residues: 35.7639 Evaluate side-chains 101 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0858 time to fit residues: 1.7726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.178 Angle : 0.443 7.447 12135 Z= 0.235 Chirality : 0.041 0.186 1352 Planarity : 0.004 0.042 1544 Dihedral : 4.133 45.489 1229 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.39 % 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 (0.25), residues: 1099 helix: 2.10 (0.23), residues: 539 sheet: -0.13 (0.44), residues: 124 loop : -0.65 (0.27), residues: 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.004 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.2306 time to fit residues: 37.5441 Evaluate side-chains 107 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0912 time to fit residues: 2.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8968 Z= 0.146 Angle : 0.435 7.732 12135 Z= 0.229 Chirality : 0.041 0.181 1352 Planarity : 0.003 0.041 1544 Dihedral : 4.034 46.319 1229 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.86 % 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: 1.22 (0.25), residues: 1099 helix: 2.13 (0.23), residues: 543 sheet: -0.09 (0.44), residues: 124 loop : -0.63 (0.28), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.047 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 108 average time/residue: 0.2140 time to fit residues: 32.5821 Evaluate side-chains 106 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0830 time to fit residues: 1.6866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8968 Z= 0.210 Angle : 0.463 8.899 12135 Z= 0.243 Chirality : 0.042 0.182 1352 Planarity : 0.003 0.042 1544 Dihedral : 4.066 45.517 1229 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.75 % 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: 1.15 (0.25), residues: 1099 helix: 2.10 (0.23), residues: 540 sheet: -0.07 (0.45), residues: 122 loop : -0.69 (0.27), residues: 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.096 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2290 time to fit residues: 33.9408 Evaluate side-chains 105 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0925 time to fit residues: 2.0665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.203 Angle : 0.473 11.724 12135 Z= 0.245 Chirality : 0.042 0.181 1352 Planarity : 0.003 0.043 1544 Dihedral : 4.082 46.082 1229 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.43 % 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: 1.13 (0.25), residues: 1099 helix: 2.12 (0.23), residues: 538 sheet: -0.18 (0.44), residues: 124 loop : -0.72 (0.27), residues: 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.091 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 100 average time/residue: 0.2296 time to fit residues: 32.3629 Evaluate side-chains 99 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0818 time to fit residues: 1.6316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8968 Z= 0.237 Angle : 0.494 11.968 12135 Z= 0.255 Chirality : 0.042 0.181 1352 Planarity : 0.004 0.044 1544 Dihedral : 4.135 45.863 1229 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.54 % 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: 1.05 (0.25), residues: 1099 helix: 2.08 (0.23), residues: 534 sheet: -0.23 (0.44), residues: 124 loop : -0.77 (0.27), residues: 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.978 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.2197 time to fit residues: 31.4991 Evaluate side-chains 98 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0980 time to fit residues: 1.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.212 Angle : 0.480 12.681 12135 Z= 0.248 Chirality : 0.042 0.180 1352 Planarity : 0.003 0.043 1544 Dihedral : 4.111 46.292 1229 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.32 % 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: 1.03 (0.25), residues: 1099 helix: 2.07 (0.23), residues: 538 sheet: -0.24 (0.44), residues: 124 loop : -0.80 (0.27), residues: 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.135 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.2293 time to fit residues: 31.4685 Evaluate side-chains 95 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 8 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8968 Z= 0.156 Angle : 0.474 13.112 12135 Z= 0.240 Chirality : 0.041 0.177 1352 Planarity : 0.003 0.041 1544 Dihedral : 4.007 46.657 1229 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.43 % 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: 1.14 (0.25), residues: 1099 helix: 2.17 (0.23), residues: 538 sheet: -0.22 (0.44), residues: 124 loop : -0.75 (0.27), residues: 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.073 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.2221 time to fit residues: 30.5838 Evaluate side-chains 96 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1157 time to fit residues: 1.8854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 62 optimal weight: 0.2980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105988 restraints weight = 13325.312| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.90 r_work: 0.3206 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8968 Z= 0.142 Angle : 0.453 13.160 12135 Z= 0.231 Chirality : 0.041 0.176 1352 Planarity : 0.003 0.037 1544 Dihedral : 3.897 46.279 1229 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.11 % 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: 1.24 (0.25), residues: 1099 helix: 2.26 (0.23), residues: 539 sheet: -0.21 (0.44), residues: 124 loop : -0.71 (0.27), residues: 436 =============================================================================== Job complete usr+sys time: 1919.62 seconds wall clock time: 36 minutes 15.03 seconds (2175.03 seconds total)