Starting phenix.real_space_refine on Wed Feb 14 04:26:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/02_2024/6jt1_9884_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "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 TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} 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: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} 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: {'peptide': 576, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552, None: 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: {'peptide': 576, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552, None: 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: 9.14, per 1000 atoms: 1.06 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 93.005, 73.15, 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 3.3 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: 42 helices and 10 sheets defined 42.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 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: 3.640A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.596A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 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: 4.472A 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 422 through 425 removed outlier: 4.509A pdb=" N LEU A 425 " --> pdb=" O GLN A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 425' Processing helix chain 'A' and resid 427 through 457 Processing helix chain 'A' and resid 460 through 468 removed outlier: 3.616A 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: 3.776A pdb=" N CYS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 4.193A 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: 3.929A 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 101 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.809A 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: 3.554A 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: 3.631A 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: 3.802A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.012A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 4.391A 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: 4.034A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 258 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.013A 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: 3.515A 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: 3.739A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.498A 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: 4.382A 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: 3.792A pdb=" N GLN B 178 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.317A 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: 3.565A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.555A 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: 3.641A 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: 6.378A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.307A 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: 2.58 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 3536 1.40 - 1.58: 5154 1.58 - 1.77: 0 1.77 - 1.95: 90 1.95 - 2.13: 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 1.269 -0.033 1.17e-02 7.31e+03 7.83e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.30e-02 5.92e+03 5.91e+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 5.13e+00 bond pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.06e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.30e-02 5.92e+03 3.82e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 86.18 - 100.57: 9 100.57 - 114.96: 5613 114.96 - 129.35: 6267 129.35 - 143.74: 44 143.74 - 158.13: 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 120.56 130.64 -10.08 1.28e+00 6.10e-01 6.20e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.27 -4.99 1.34e+00 5.57e-01 1.39e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA ALA B 103 " pdb=" C ALA B 103 " pdb=" N LEU B 104 " ideal model delta sigma weight residual 117.30 113.72 3.58 1.16e+00 7.43e-01 9.50e+00 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4901 17.82 - 35.64: 284 35.64 - 53.46: 47 53.46 - 71.28: 17 71.28 - 89.10: 3 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 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER B 209 " pdb=" C SER B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+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 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 837 0.034 - 0.067: 389 0.067 - 0.101: 116 0.101 - 0.134: 41 0.134 - 0.168: 7 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA HIS B 105 " pdb=" N HIS B 105 " pdb=" C HIS B 105 " pdb=" CB HIS B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 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 2.55 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE B 343 " pdb=" N ILE B 343 " pdb=" C ILE B 343 " pdb=" CB ILE B 343 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 113 " 0.075 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=" CA ASP B 452 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASP B 452 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 452 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 453 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 453 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LEU B 453 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU B 453 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 454 " -0.010 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 927 2.75 - 3.29: 8642 3.29 - 3.82: 13947 3.82 - 4.36: 16081 4.36 - 4.90: 27343 Nonbonded interactions: 66940 Sorted by model distance: nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.212 2.520 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.254 2.440 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.274 2.440 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.290 2.520 nonbonded pdb=" O VAL A 154 " pdb=" N LEU B 340 " model vdw 2.294 2.520 ... (remaining 66935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.040 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 0.056 8784 Z= 0.254 Angle : 0.770 23.695 11935 Z= 0.392 Chirality : 0.044 0.168 1390 Planarity : 0.004 0.043 1515 Dihedral : 12.201 89.097 3144 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.82 % Favored : 93.82 % Rotamer: Outliers : 4.62 % Allowed : 6.15 % Favored : 89.23 % 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: -2.92 (0.22), residues: 1101 helix: -1.13 (0.20), residues: 506 sheet: -2.21 (0.31), residues: 212 loop : -2.67 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 22 HIS 0.005 0.001 HIS B 176 PHE 0.025 0.002 PHE A 458 TYR 0.017 0.002 TYR B 454 ARG 0.002 0.000 ARG B 360 *********************** 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 213 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9258 (mttm) cc_final: 0.9005 (mtmm) REVERT: A 159 LEU cc_start: 0.8786 (pp) cc_final: 0.8431 (tt) REVERT: A 161 ASP cc_start: 0.8632 (m-30) cc_final: 0.8404 (m-30) REVERT: A 209 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8715 (tpt170) REVERT: A 252 TYR cc_start: 0.8984 (p90) cc_final: 0.8368 (p90) REVERT: A 351 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7693 (ptt-90) REVERT: A 364 MET cc_start: 0.8900 (ttp) cc_final: 0.8442 (ttp) REVERT: A 573 MET cc_start: 0.8673 (mmm) cc_final: 0.8303 (tpt) REVERT: A 583 PHE cc_start: 0.9178 (m-80) cc_final: 0.8937 (m-10) REVERT: A 606 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8669 (tppt) REVERT: A 645 ASN cc_start: 0.9225 (m-40) cc_final: 0.8859 (p0) REVERT: A 656 PHE cc_start: 0.8463 (m-80) cc_final: 0.7768 (m-80) REVERT: B 62 ASN cc_start: 0.7387 (m110) cc_final: 0.6870 (t0) REVERT: B 65 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8065 (tp30) REVERT: B 328 MET cc_start: 0.8442 (mtm) cc_final: 0.8208 (mtm) REVERT: B 335 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8434 (mtm-85) REVERT: B 379 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 386 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9069 (mp0) REVERT: B 471 LYS cc_start: 0.9182 (tttm) cc_final: 0.8892 (tttp) REVERT: B 569 TYR cc_start: 0.8503 (t80) cc_final: 0.7993 (t80) REVERT: B 571 CYS cc_start: 0.9354 (m) cc_final: 0.9101 (m) REVERT: B 581 GLN cc_start: 0.9383 (mt0) cc_final: 0.8994 (tp-100) REVERT: B 584 LEU cc_start: 0.9638 (mm) cc_final: 0.9418 (mm) outliers start: 42 outliers final: 20 residues processed: 204 average time/residue: 0.1821 time to fit residues: 53.0806 Evaluate side-chains 127 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 449 LEU 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 465 GLN B 93 ASN B 134 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0.7987 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8784 Z= 0.208 Angle : 0.702 18.871 11935 Z= 0.326 Chirality : 0.043 0.204 1390 Planarity : 0.004 0.046 1515 Dihedral : 7.982 80.521 1241 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 4.84 % Allowed : 12.86 % Favored : 82.31 % 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: -1.70 (0.24), residues: 1101 helix: -0.06 (0.22), residues: 505 sheet: -1.54 (0.33), residues: 214 loop : -2.20 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.013 0.001 HIS A 100 PHE 0.013 0.002 PHE A 335 TYR 0.017 0.001 TYR B 237 ARG 0.005 0.000 ARG B 416 *********************** 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 160 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 116 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8309 (ttm170) REVERT: A 142 LYS cc_start: 0.9256 (mttm) cc_final: 0.8999 (mtmm) REVERT: A 159 LEU cc_start: 0.8719 (pp) cc_final: 0.8418 (tt) REVERT: A 209 ARG cc_start: 0.9049 (mtt180) cc_final: 0.8712 (tpt170) REVERT: A 281 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8223 (tm) REVERT: A 291 MET cc_start: 0.9443 (ttp) cc_final: 0.9221 (mtm) REVERT: A 351 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7681 (ptm-80) REVERT: A 573 MET cc_start: 0.8491 (mmm) cc_final: 0.8149 (tpt) REVERT: A 583 PHE cc_start: 0.9162 (m-80) cc_final: 0.8901 (m-10) REVERT: A 607 PHE cc_start: 0.8815 (m-80) cc_final: 0.8411 (t80) REVERT: A 645 ASN cc_start: 0.9231 (m-40) cc_final: 0.8867 (p0) REVERT: B 62 ASN cc_start: 0.7436 (m110) cc_final: 0.6963 (t0) REVERT: B 65 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8066 (tp30) REVERT: B 69 MET cc_start: 0.8748 (mtp) cc_final: 0.8524 (mtm) REVERT: B 335 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8458 (mtm-85) REVERT: B 386 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9046 (mp0) REVERT: B 444 MET cc_start: 0.8599 (tmm) cc_final: 0.7998 (mtt) REVERT: B 458 ASP cc_start: 0.9412 (m-30) cc_final: 0.9097 (m-30) REVERT: B 471 LYS cc_start: 0.9117 (tttm) cc_final: 0.8896 (tttp) REVERT: B 569 TYR cc_start: 0.8442 (t80) cc_final: 0.8081 (t80) REVERT: B 571 CYS cc_start: 0.9276 (m) cc_final: 0.9000 (m) REVERT: B 581 GLN cc_start: 0.9392 (mt0) cc_final: 0.9005 (tp-100) REVERT: B 592 MET cc_start: 0.7655 (mtm) cc_final: 0.7267 (mtm) REVERT: B 599 MET cc_start: 0.8192 (ttt) cc_final: 0.7692 (ttt) outliers start: 44 outliers final: 30 residues processed: 151 average time/residue: 0.1918 time to fit residues: 40.9617 Evaluate side-chains 129 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 249 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 563 ASN ** 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: 0.7977 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.191 Angle : 0.687 16.109 11935 Z= 0.317 Chirality : 0.042 0.188 1390 Planarity : 0.004 0.055 1515 Dihedral : 7.377 76.082 1232 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 4.29 % Allowed : 14.29 % Favored : 81.43 % 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: -0.94 (0.25), residues: 1101 helix: 0.61 (0.23), residues: 499 sheet: -1.23 (0.34), residues: 214 loop : -1.80 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.014 0.001 HIS A 100 PHE 0.024 0.002 PHE A 656 TYR 0.015 0.001 TYR B 339 ARG 0.003 0.000 ARG B 416 *********************** 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 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9250 (mttm) cc_final: 0.9019 (mtmm) REVERT: A 159 LEU cc_start: 0.8746 (pp) cc_final: 0.8448 (tt) REVERT: A 209 ARG cc_start: 0.9049 (mtt180) cc_final: 0.8705 (tpt170) REVERT: A 281 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8235 (tm) REVERT: A 291 MET cc_start: 0.9474 (ttp) cc_final: 0.9191 (mtm) REVERT: A 351 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7646 (ptm-80) REVERT: A 583 PHE cc_start: 0.9188 (m-80) cc_final: 0.8952 (m-10) REVERT: A 645 ASN cc_start: 0.9244 (m-40) cc_final: 0.8865 (p0) REVERT: B 62 ASN cc_start: 0.7489 (m110) cc_final: 0.7104 (t0) REVERT: B 65 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7974 (tp30) REVERT: B 335 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8470 (mtm-85) REVERT: B 386 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9038 (mp0) REVERT: B 444 MET cc_start: 0.8592 (tmm) cc_final: 0.7930 (mtt) REVERT: B 458 ASP cc_start: 0.9449 (m-30) cc_final: 0.9033 (m-30) REVERT: B 471 LYS cc_start: 0.9087 (tttm) cc_final: 0.8861 (tttp) REVERT: B 569 TYR cc_start: 0.8320 (t80) cc_final: 0.8117 (t80) REVERT: B 571 CYS cc_start: 0.9094 (m) cc_final: 0.8836 (m) REVERT: B 592 MET cc_start: 0.7580 (mtm) cc_final: 0.7260 (mtm) REVERT: B 599 MET cc_start: 0.8246 (ttt) cc_final: 0.7921 (ttt) outliers start: 39 outliers final: 28 residues processed: 140 average time/residue: 0.1874 time to fit residues: 37.4179 Evaluate side-chains 129 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 11 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0.7956 moved from start: 0.2362 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= 0.172 Angle : 0.669 13.532 11935 Z= 0.306 Chirality : 0.042 0.170 1390 Planarity : 0.004 0.049 1515 Dihedral : 6.948 76.823 1229 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.29 % Allowed : 15.49 % Favored : 80.22 % 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: -0.49 (0.25), residues: 1101 helix: 0.89 (0.23), residues: 514 sheet: -0.76 (0.35), residues: 216 loop : -1.71 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.005 0.001 HIS A 545 PHE 0.017 0.001 PHE A 83 TYR 0.016 0.001 TYR B 339 ARG 0.003 0.000 ARG A 639 *********************** 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 157 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9242 (mttm) cc_final: 0.9024 (mtmm) REVERT: A 159 LEU cc_start: 0.8675 (pp) cc_final: 0.8407 (tt) REVERT: A 209 ARG cc_start: 0.9068 (mtt180) cc_final: 0.8698 (tpt170) REVERT: A 281 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8249 (tm) REVERT: A 291 MET cc_start: 0.9440 (ttp) cc_final: 0.9195 (mtm) REVERT: A 351 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7606 (ptm-80) REVERT: A 573 MET cc_start: 0.8410 (mmm) cc_final: 0.8097 (tpt) REVERT: A 583 PHE cc_start: 0.9241 (m-80) cc_final: 0.8969 (m-10) REVERT: A 645 ASN cc_start: 0.9235 (m-40) cc_final: 0.8840 (p0) REVERT: B 62 ASN cc_start: 0.7580 (m110) cc_final: 0.7239 (t0) REVERT: B 65 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7897 (tp30) REVERT: B 335 ARG cc_start: 0.8826 (mtt180) cc_final: 0.8466 (mtm-85) REVERT: B 347 ASP cc_start: 0.8217 (t0) cc_final: 0.7923 (t0) REVERT: B 386 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9002 (mp0) REVERT: B 444 MET cc_start: 0.8585 (tmm) cc_final: 0.7955 (mtt) REVERT: B 471 LYS cc_start: 0.9047 (tttm) cc_final: 0.8813 (tttp) REVERT: B 571 CYS cc_start: 0.9124 (m) cc_final: 0.8846 (m) REVERT: B 592 MET cc_start: 0.7486 (mtm) cc_final: 0.7144 (mtm) REVERT: B 599 MET cc_start: 0.8291 (ttt) cc_final: 0.7972 (ttt) outliers start: 39 outliers final: 29 residues processed: 150 average time/residue: 0.1806 time to fit residues: 39.1704 Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.197 Angle : 0.671 13.546 11935 Z= 0.308 Chirality : 0.042 0.242 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.912 76.513 1227 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.95 % Allowed : 15.38 % Favored : 79.67 % 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: -0.24 (0.26), residues: 1101 helix: 1.11 (0.23), residues: 515 sheet: -0.67 (0.36), residues: 209 loop : -1.58 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 655 PHE 0.014 0.001 PHE A 83 TYR 0.032 0.001 TYR B 569 ARG 0.003 0.000 ARG B 570 *********************** 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 157 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8717 (pp) cc_final: 0.8457 (tt) REVERT: A 209 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8681 (tpt170) REVERT: A 281 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8216 (tm) REVERT: A 351 ARG cc_start: 0.7942 (ptm160) cc_final: 0.7557 (ptm-80) REVERT: A 573 MET cc_start: 0.8416 (mmm) cc_final: 0.7984 (tpt) REVERT: A 583 PHE cc_start: 0.9231 (m-80) cc_final: 0.8914 (m-10) REVERT: A 645 ASN cc_start: 0.9205 (m-40) cc_final: 0.8808 (p0) REVERT: B 62 ASN cc_start: 0.7424 (m110) cc_final: 0.7092 (t0) REVERT: B 65 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8053 (tp30) REVERT: B 335 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8489 (mtm-85) REVERT: B 347 ASP cc_start: 0.8209 (t0) cc_final: 0.7899 (t0) REVERT: B 386 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: B 444 MET cc_start: 0.8601 (tmm) cc_final: 0.7937 (mtt) REVERT: B 471 LYS cc_start: 0.9055 (tttm) cc_final: 0.8819 (tttp) REVERT: B 571 CYS cc_start: 0.9281 (m) cc_final: 0.8996 (m) REVERT: B 592 MET cc_start: 0.7537 (mtm) cc_final: 0.7212 (mtm) REVERT: B 599 MET cc_start: 0.8304 (ttt) cc_final: 0.7977 (ttt) outliers start: 45 outliers final: 37 residues processed: 149 average time/residue: 0.1826 time to fit residues: 39.2325 Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 102 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0670 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8784 Z= 0.257 Angle : 0.692 14.486 11935 Z= 0.321 Chirality : 0.043 0.236 1390 Planarity : 0.004 0.052 1515 Dihedral : 6.810 75.775 1226 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.73 % Rotamer: Outliers : 5.05 % Allowed : 16.04 % Favored : 78.90 % 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: -0.09 (0.26), residues: 1101 helix: 1.24 (0.23), residues: 511 sheet: -0.66 (0.36), residues: 209 loop : -1.46 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 602 HIS 0.004 0.001 HIS A 655 PHE 0.021 0.002 PHE B 603 TYR 0.037 0.002 TYR B 569 ARG 0.004 0.000 ARG B 40 *********************** 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 148 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 102 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8722 (pp) cc_final: 0.8420 (tt) REVERT: A 209 ARG cc_start: 0.9068 (mtt180) cc_final: 0.8679 (tpt170) REVERT: A 556 MET cc_start: 0.9468 (ttm) cc_final: 0.9123 (mmm) REVERT: A 573 MET cc_start: 0.8559 (mmm) cc_final: 0.8241 (tpt) REVERT: A 583 PHE cc_start: 0.9226 (m-80) cc_final: 0.8895 (m-10) REVERT: A 645 ASN cc_start: 0.9232 (m-40) cc_final: 0.8815 (p0) REVERT: B 44 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8373 (p0) REVERT: B 62 ASN cc_start: 0.7535 (m110) cc_final: 0.7215 (t0) REVERT: B 65 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8044 (tp30) REVERT: B 335 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8494 (mtm-85) REVERT: B 340 LEU cc_start: 0.8327 (tt) cc_final: 0.7841 (tp) REVERT: B 347 ASP cc_start: 0.8074 (t0) cc_final: 0.7763 (t0) REVERT: B 386 GLU cc_start: 0.9481 (OUTLIER) cc_final: 0.9131 (mp0) REVERT: B 444 MET cc_start: 0.8606 (tmm) cc_final: 0.7933 (mtt) REVERT: B 471 LYS cc_start: 0.9091 (tttm) cc_final: 0.8837 (tttp) REVERT: B 571 CYS cc_start: 0.9305 (m) cc_final: 0.8991 (m) REVERT: B 592 MET cc_start: 0.7638 (mtm) cc_final: 0.7321 (mtm) REVERT: B 599 MET cc_start: 0.8288 (ttt) cc_final: 0.7973 (ttt) outliers start: 46 outliers final: 41 residues processed: 137 average time/residue: 0.1761 time to fit residues: 35.5408 Evaluate side-chains 142 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.0070 chunk 59 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0.7949 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8784 Z= 0.157 Angle : 0.664 15.512 11935 Z= 0.300 Chirality : 0.042 0.265 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.590 77.504 1226 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 16.37 % Favored : 79.56 % 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: 0.10 (0.26), residues: 1101 helix: 1.36 (0.24), residues: 514 sheet: -0.39 (0.35), residues: 217 loop : -1.44 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 467 HIS 0.004 0.001 HIS A 655 PHE 0.013 0.001 PHE B 321 TYR 0.027 0.001 TYR A 623 ARG 0.002 0.000 ARG B 416 *********************** 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 145 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8696 (pp) cc_final: 0.8425 (tt) REVERT: A 209 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8671 (tpt170) REVERT: A 556 MET cc_start: 0.9522 (ttm) cc_final: 0.9205 (mmm) REVERT: A 583 PHE cc_start: 0.9238 (m-80) cc_final: 0.8889 (m-10) REVERT: A 593 ARG cc_start: 0.9255 (mtt-85) cc_final: 0.7879 (ptm-80) REVERT: A 645 ASN cc_start: 0.9194 (m-40) cc_final: 0.8745 (p0) REVERT: B 62 ASN cc_start: 0.7704 (m110) cc_final: 0.7416 (t0) REVERT: B 65 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8011 (tp30) REVERT: B 335 ARG cc_start: 0.8833 (mtt180) cc_final: 0.8511 (mtm-85) REVERT: B 347 ASP cc_start: 0.8164 (t0) cc_final: 0.7842 (t0) REVERT: B 386 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.8691 (tp30) REVERT: B 444 MET cc_start: 0.8562 (tmm) cc_final: 0.7886 (mtt) REVERT: B 471 LYS cc_start: 0.9032 (tttm) cc_final: 0.8791 (tttp) REVERT: B 480 MET cc_start: 0.9583 (ttt) cc_final: 0.9357 (ttt) REVERT: B 571 CYS cc_start: 0.9249 (m) cc_final: 0.8913 (m) REVERT: B 592 MET cc_start: 0.7648 (mtm) cc_final: 0.7343 (mtm) REVERT: B 599 MET cc_start: 0.8388 (ttt) cc_final: 0.8056 (ttt) outliers start: 37 outliers final: 35 residues processed: 136 average time/residue: 0.1723 time to fit residues: 33.9272 Evaluate side-chains 138 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN 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: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.0370 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 97 optimal weight: 0.0670 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0.7941 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8784 Z= 0.159 Angle : 0.666 14.412 11935 Z= 0.299 Chirality : 0.041 0.260 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.317 77.982 1223 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.96 % Allowed : 17.03 % Favored : 79.01 % 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: 0.23 (0.26), residues: 1101 helix: 1.42 (0.24), residues: 514 sheet: -0.27 (0.35), residues: 217 loop : -1.35 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.003 0.001 HIS A 655 PHE 0.013 0.001 PHE B 603 TYR 0.028 0.001 TYR A 623 ARG 0.003 0.000 ARG B 606 *********************** 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 144 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8696 (pp) cc_final: 0.8408 (tt) REVERT: A 209 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8671 (tpt170) REVERT: A 556 MET cc_start: 0.9480 (ttm) cc_final: 0.9142 (mmm) REVERT: A 583 PHE cc_start: 0.9240 (m-80) cc_final: 0.8884 (m-10) REVERT: A 593 ARG cc_start: 0.9234 (mtt-85) cc_final: 0.7865 (ptm-80) REVERT: A 607 PHE cc_start: 0.8771 (m-80) cc_final: 0.8498 (m-80) REVERT: A 645 ASN cc_start: 0.9193 (m-40) cc_final: 0.8723 (p0) REVERT: B 62 ASN cc_start: 0.7674 (m110) cc_final: 0.7404 (t0) REVERT: B 65 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8041 (tp30) REVERT: B 335 ARG cc_start: 0.8833 (mtt180) cc_final: 0.8276 (mmp-170) REVERT: B 347 ASP cc_start: 0.8162 (t0) cc_final: 0.7858 (t0) REVERT: B 386 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: B 444 MET cc_start: 0.8576 (tmm) cc_final: 0.7923 (mtt) REVERT: B 471 LYS cc_start: 0.9027 (tttm) cc_final: 0.8784 (tttp) REVERT: B 571 CYS cc_start: 0.9250 (m) cc_final: 0.8942 (m) REVERT: B 573 MET cc_start: 0.8799 (mmp) cc_final: 0.8470 (mmp) REVERT: B 592 MET cc_start: 0.7640 (mtm) cc_final: 0.7340 (mtm) REVERT: B 599 MET cc_start: 0.8407 (ttt) cc_final: 0.8058 (ttt) outliers start: 36 outliers final: 31 residues processed: 134 average time/residue: 0.1824 time to fit residues: 35.5204 Evaluate side-chains 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0370 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.0000 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8784 Z= 0.151 Angle : 0.658 13.251 11935 Z= 0.296 Chirality : 0.041 0.285 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.225 80.100 1222 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.97 % Allowed : 18.02 % Favored : 79.01 % 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: 0.37 (0.26), residues: 1101 helix: 1.53 (0.24), residues: 509 sheet: -0.09 (0.36), residues: 217 loop : -1.33 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 602 HIS 0.003 0.001 HIS A 655 PHE 0.014 0.001 PHE A 83 TYR 0.025 0.001 TYR A 623 ARG 0.003 0.000 ARG B 570 *********************** 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 143 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8674 (pp) cc_final: 0.8423 (tt) REVERT: A 209 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8645 (tpt170) REVERT: A 343 ASN cc_start: 0.8819 (t0) cc_final: 0.8588 (t0) REVERT: A 556 MET cc_start: 0.9458 (ttm) cc_final: 0.8668 (mmm) REVERT: A 557 MET cc_start: 0.9526 (mmm) cc_final: 0.9052 (mmm) REVERT: A 583 PHE cc_start: 0.9242 (m-80) cc_final: 0.8886 (m-10) REVERT: A 593 ARG cc_start: 0.9188 (mtt-85) cc_final: 0.7862 (ptm-80) REVERT: A 645 ASN cc_start: 0.9152 (m-40) cc_final: 0.8631 (p0) REVERT: B 62 ASN cc_start: 0.7731 (m110) cc_final: 0.7494 (t0) REVERT: B 65 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7909 (tp30) REVERT: B 335 ARG cc_start: 0.8824 (mtt180) cc_final: 0.8287 (mmp-170) REVERT: B 347 ASP cc_start: 0.8144 (t0) cc_final: 0.7645 (t0) REVERT: B 386 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: B 444 MET cc_start: 0.8591 (tmm) cc_final: 0.7925 (mtt) REVERT: B 471 LYS cc_start: 0.8972 (tttm) cc_final: 0.8658 (tttp) REVERT: B 480 MET cc_start: 0.9562 (ttt) cc_final: 0.9322 (ttt) REVERT: B 571 CYS cc_start: 0.9281 (m) cc_final: 0.8982 (m) REVERT: B 573 MET cc_start: 0.8791 (mmp) cc_final: 0.8508 (mmp) REVERT: B 592 MET cc_start: 0.7621 (mtm) cc_final: 0.7323 (mtm) REVERT: B 599 MET cc_start: 0.8389 (ttt) cc_final: 0.7971 (ttt) outliers start: 27 outliers final: 24 residues processed: 134 average time/residue: 0.1873 time to fit residues: 35.7444 Evaluate side-chains 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.0670 chunk 110 optimal weight: 0.0030 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8784 Z= 0.157 Angle : 0.664 13.264 11935 Z= 0.299 Chirality : 0.041 0.260 1390 Planarity : 0.004 0.047 1515 Dihedral : 6.131 80.685 1218 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.86 % Allowed : 19.01 % Favored : 78.13 % 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: 0.47 (0.26), residues: 1101 helix: 1.62 (0.24), residues: 508 sheet: 0.03 (0.36), residues: 217 loop : -1.34 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 467 HIS 0.003 0.001 HIS A 655 PHE 0.034 0.001 PHE A 141 TYR 0.024 0.001 TYR A 623 ARG 0.002 0.000 ARG B 416 ********************** 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 133 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8658 (pp) cc_final: 0.8405 (tt) REVERT: A 209 ARG cc_start: 0.9036 (mtt180) cc_final: 0.8642 (tpt170) REVERT: A 343 ASN cc_start: 0.8831 (t0) cc_final: 0.8616 (t0) REVERT: A 467 TRP cc_start: 0.8640 (t60) cc_final: 0.8345 (t60) REVERT: A 556 MET cc_start: 0.9450 (ttm) cc_final: 0.8695 (mmm) REVERT: A 557 MET cc_start: 0.9478 (mmm) cc_final: 0.9006 (mmm) REVERT: A 583 PHE cc_start: 0.9249 (m-80) cc_final: 0.8886 (m-10) REVERT: A 593 ARG cc_start: 0.9195 (mtt-85) cc_final: 0.7802 (ptm-80) REVERT: A 645 ASN cc_start: 0.9121 (m-40) cc_final: 0.8588 (p0) REVERT: B 62 ASN cc_start: 0.7712 (m110) cc_final: 0.7476 (t0) REVERT: B 65 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7903 (tp30) REVERT: B 335 ARG cc_start: 0.8809 (mtt180) cc_final: 0.8312 (mmp-170) REVERT: B 347 ASP cc_start: 0.8143 (t0) cc_final: 0.7636 (t0) REVERT: B 386 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.8965 (mp0) REVERT: B 444 MET cc_start: 0.8604 (tmm) cc_final: 0.7939 (mtt) REVERT: B 471 LYS cc_start: 0.9012 (tttm) cc_final: 0.8689 (tttp) REVERT: B 480 MET cc_start: 0.9568 (ttt) cc_final: 0.9315 (ttt) REVERT: B 571 CYS cc_start: 0.9240 (m) cc_final: 0.8946 (m) REVERT: B 573 MET cc_start: 0.8729 (mmp) cc_final: 0.8413 (mmp) REVERT: B 592 MET cc_start: 0.7644 (mtm) cc_final: 0.7329 (mtm) REVERT: B 599 MET cc_start: 0.8388 (ttt) cc_final: 0.8029 (ttt) outliers start: 26 outliers final: 25 residues processed: 124 average time/residue: 0.2058 time to fit residues: 36.6133 Evaluate side-chains 129 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077479 restraints weight = 20784.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079740 restraints weight = 12303.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080766 restraints weight = 8386.058| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8784 Z= 0.254 Angle : 0.705 17.161 11935 Z= 0.321 Chirality : 0.042 0.230 1390 Planarity : 0.004 0.051 1515 Dihedral : 6.168 75.342 1218 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.86 % Allowed : 19.12 % Favored : 78.02 % 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: 0.37 (0.26), residues: 1101 helix: 1.55 (0.24), residues: 518 sheet: -0.10 (0.36), residues: 217 loop : -1.42 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 467 HIS 0.004 0.001 HIS B 260 PHE 0.023 0.002 PHE A 141 TYR 0.024 0.002 TYR A 623 ARG 0.002 0.000 ARG B 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.25 seconds wall clock time: 36 minutes 11.95 seconds (2171.95 seconds total)