Starting phenix.real_space_refine (version: dev) on Thu May 12 22:31:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/05_2022/6jt0_9883_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 25, 'TRANS': 515, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 25, 'TRANS': 515, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 4165 Chain: "B" Number of atoms: 4515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4511 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1, 'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 552, None: 1, 'PCIS': 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 577, 4511 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1, 'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 552, None: 1, 'PCIS': 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 4603 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 Time building chain proxies: 9.21, per 1000 atoms: 1.07 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 96.14, 74.195, 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) Fe 1 26.01 S 59 16.00 O 1551 8.00 N 1462 7.00 C 5529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 10 sheets defined 42.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 148 removed outlier: 3.588A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.471A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Processing helix chain 'A' and resid 460 through 468 removed outlier: 3.621A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 499 through 520 Processing helix chain 'A' and resid 545 through 560 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.773A pdb=" N CYS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.912A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Proline residue: B 19 - end of helix removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 80 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.871A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.562A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 360 through 394 removed outlier: 3.608A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 440 through 460 removed outlier: 3.709A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.028A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.003A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 258 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.520A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 480 through 482 Processing sheet with id= E, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.741A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 616 through 618 removed outlier: 4.313A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.761A pdb=" N GLN B 178 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.613A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.758A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.462A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1097 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: 2.68 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3085 1.38 - 1.55: 5579 1.55 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 4 Bond restraints: 8784 Sorted by residual: bond pdb=" C ASP B 106 " pdb=" O ASP B 106 " ideal model delta sigma weight residual 1.237 1.266 -0.029 1.17e-02 7.31e+03 6.10e+00 bond pdb=" C ALA B 103 " pdb=" O ALA B 103 " ideal model delta sigma weight residual 1.237 1.263 -0.026 1.17e-02 7.31e+03 4.90e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.30e-02 5.92e+03 4.74e+00 bond pdb=" CA GLU A 230 " pdb=" CB GLU A 230 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.22e-02 6.72e+03 4.62e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.30e-02 5.92e+03 4.59e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 89.05 - 106.50: 265 106.50 - 123.94: 11439 123.94 - 141.39: 229 141.39 - 158.84: 0 158.84 - 176.29: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" C THR B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.56 130.79 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 108.17 115.21 -7.04 1.46e+00 4.69e-01 2.33e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.10 -4.82 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N TYR B 395 " pdb=" CA TYR B 395 " pdb=" C TYR B 395 " ideal model delta sigma weight residual 110.06 115.00 -4.94 1.43e+00 4.89e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4896 17.53 - 35.05: 289 35.05 - 52.58: 48 52.58 - 70.10: 12 70.10 - 87.63: 7 Dihedral angle restraints: 5252 sinusoidal: 1996 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA HIS A 655 " pdb=" C HIS A 655 " pdb=" N PHE A 656 " pdb=" CA PHE A 656 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1037 0.044 - 0.088: 264 0.088 - 0.132: 82 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU B 9 " pdb=" CB LEU B 9 " pdb=" CD1 LEU B 9 " pdb=" CD2 LEU B 9 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 250 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 251 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 113 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 328 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 329 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.020 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 896 2.75 - 3.29: 8652 3.29 - 3.82: 14007 3.82 - 4.36: 16122 4.36 - 4.90: 27413 Nonbonded interactions: 67090 Sorted by model distance: nonbonded pdb=" O TYR A 623 " pdb=" N LYS A 627 " model vdw 2.212 2.520 nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.225 2.520 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.267 2.440 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.295 2.520 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.309 2.440 ... (remaining 67085 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 Fe 1 7.16 5 S 59 5.16 5 C 5529 2.51 5 N 1462 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 3.560 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 31.670 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.004 0.100 8784 Z= 0.238 Angle : 0.710 10.228 11935 Z= 0.391 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.057 1515 Dihedral : 12.208 87.630 3144 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.73 % Favored : 93.91 % Rotamer Outliers : 4.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -2.84 (0.22), residues: 1101 helix: -1.01 (0.20), residues: 505 sheet: -2.10 (0.31), residues: 211 loop : -2.74 (0.27), residues: 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 178 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 11 residues processed: 211 average time/residue: 0.1814 time to fit residues: 54.2053 Evaluate side-chains 103 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1207 time to fit residues: 3.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.0370 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 367 GLN B 518 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 8784 Z= 0.219 Angle : 0.804 14.360 11935 Z= 0.372 Chirality : 0.045 0.218 1390 Planarity : 0.005 0.077 1515 Dihedral : 6.174 81.237 1206 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.73 % Favored : 95.00 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.61 (0.24), residues: 1101 helix: 0.10 (0.22), residues: 507 sheet: -1.51 (0.31), residues: 228 loop : -2.32 (0.29), residues: 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 117 average time/residue: 0.1723 time to fit residues: 30.1067 Evaluate side-chains 91 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1197 time to fit residues: 2.9531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8784 Z= 0.192 Angle : 0.748 12.939 11935 Z= 0.341 Chirality : 0.043 0.170 1390 Planarity : 0.004 0.054 1515 Dihedral : 5.547 79.303 1206 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.89 (0.25), residues: 1101 helix: 0.75 (0.23), residues: 510 sheet: -1.16 (0.33), residues: 222 loop : -2.06 (0.30), residues: 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 108 average time/residue: 0.1682 time to fit residues: 27.2928 Evaluate side-chains 94 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1348 time to fit residues: 3.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8784 Z= 0.243 Angle : 0.755 12.236 11935 Z= 0.349 Chirality : 0.044 0.261 1390 Planarity : 0.004 0.046 1515 Dihedral : 5.451 77.746 1206 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.91 % Favored : 94.91 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.44 (0.26), residues: 1101 helix: 1.22 (0.24), residues: 506 sheet: -1.00 (0.33), residues: 228 loop : -1.92 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 0.1562 time to fit residues: 24.0583 Evaluate side-chains 89 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0779 time to fit residues: 2.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8784 Z= 0.235 Angle : 0.712 12.113 11935 Z= 0.332 Chirality : 0.043 0.174 1390 Planarity : 0.004 0.043 1515 Dihedral : 5.379 75.412 1206 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.45 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.20 (0.26), residues: 1101 helix: 1.39 (0.24), residues: 503 sheet: -0.81 (0.33), residues: 227 loop : -1.78 (0.32), residues: 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.1601 time to fit residues: 25.1156 Evaluate side-chains 87 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0876 time to fit residues: 2.2201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.181 Angle : 0.756 13.834 11935 Z= 0.342 Chirality : 0.043 0.300 1390 Planarity : 0.004 0.040 1515 Dihedral : 5.300 74.846 1206 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.02 (0.26), residues: 1101 helix: 1.41 (0.24), residues: 510 sheet: -0.56 (0.34), residues: 223 loop : -1.68 (0.32), residues: 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 0.1583 time to fit residues: 22.7577 Evaluate side-chains 83 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0993 time to fit residues: 1.9319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.203 Angle : 0.735 12.514 11935 Z= 0.335 Chirality : 0.043 0.251 1390 Planarity : 0.004 0.040 1515 Dihedral : 5.305 74.345 1206 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.08 (0.26), residues: 1101 helix: 1.48 (0.24), residues: 503 sheet: -0.52 (0.34), residues: 229 loop : -1.54 (0.33), residues: 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.1682 time to fit residues: 22.1229 Evaluate side-chains 85 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0901 time to fit residues: 2.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.203 Angle : 0.775 15.307 11935 Z= 0.347 Chirality : 0.043 0.244 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.286 73.584 1206 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.08 (0.26), residues: 1101 helix: 1.32 (0.24), residues: 519 sheet: -0.42 (0.35), residues: 227 loop : -1.46 (0.34), residues: 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 85 average time/residue: 0.1603 time to fit residues: 21.1838 Evaluate side-chains 80 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0823 time to fit residues: 1.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 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 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.176 Angle : 0.728 13.018 11935 Z= 0.328 Chirality : 0.043 0.222 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.217 72.887 1206 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.18 (0.27), residues: 1101 helix: 1.36 (0.24), residues: 518 sheet: -0.32 (0.35), residues: 227 loop : -1.39 (0.34), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.1692 time to fit residues: 22.3802 Evaluate side-chains 81 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0863 time to fit residues: 1.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 645 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.188 Angle : 0.768 14.535 11935 Z= 0.344 Chirality : 0.042 0.231 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.219 72.434 1206 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.32 (0.27), residues: 1101 helix: 1.42 (0.24), residues: 515 sheet: -0.26 (0.35), residues: 227 loop : -1.18 (0.35), residues: 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.1680 time to fit residues: 22.0626 Evaluate side-chains 82 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0818 time to fit residues: 1.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047278 restraints weight = 42468.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048862 restraints weight = 24178.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049973 restraints weight = 16245.860| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.178 Angle : 0.750 20.725 11935 Z= 0.335 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.159 72.055 1206 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.36 (0.27), residues: 1101 helix: 1.38 (0.24), residues: 520 sheet: -0.21 (0.35), residues: 227 loop : -1.09 (0.36), residues: 354 =============================================================================== Job complete usr+sys time: 1683.61 seconds wall clock time: 31 minutes 33.11 seconds (1893.11 seconds total)