Starting phenix.real_space_refine on Thu Feb 15 08:55:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p25_20236/02_2024/6p25_20236_neut_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.007 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 P 4 5.49 5 S 62 5.16 5 C 7739 2.51 5 N 1891 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5879 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 31, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5605 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain breaks: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'CPL': 1, 'NAG': 1, 'NNM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'CPL': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.74, per 1000 atoms: 0.57 Number of scatterers: 11739 At special positions: 0 Unit cell: (109.074, 107.016, 108.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 4 15.00 O 2043 8.00 N 1891 7.00 C 7739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 511 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 390 " " NAG B1001 " - " ASN B 131 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 12 sheets defined 46.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 101 through 113 removed outlier: 4.838A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 removed outlier: 4.430A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 188 through 207 Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 237 through 257 Processing helix chain 'A' and resid 263 through 295 removed outlier: 4.324A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 456 through 459 No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 533 through 549 Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.526A pdb=" N TRP A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Proline residue: A 565 - end of helix No H-bonds generated for 'chain 'A' and resid 561 through 566' Processing helix chain 'A' and resid 587 through 613 removed outlier: 4.167A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 653 through 655 No H-bonds generated for 'chain 'A' and resid 653 through 655' Processing helix chain 'A' and resid 657 through 676 removed outlier: 3.780A pdb=" N PHE A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 703 Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 715 through 721 removed outlier: 3.930A pdb=" N LYS A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'B' and resid 58 through 79 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.667A pdb=" N LYS B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 148 through 172 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 251 through 272 removed outlier: 4.087A pdb=" N ILE B 256 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 260 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.700A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 548 through 566 Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 610 through 633 removed outlier: 3.562A pdb=" N ALA B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 651 Processing helix chain 'B' and resid 653 through 668 Proline residue: B 665 - end of helix Processing helix chain 'B' and resid 675 through 694 removed outlier: 3.735A pdb=" N LEU B 679 " --> pdb=" O HIS B 676 " (cutoff:3.500A) Proline residue: B 680 - end of helix removed outlier: 4.004A pdb=" N PHE B 684 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 704 through 727 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.596A pdb=" N PHE B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 334 through 337 Processing sheet with id= C, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.750A pdb=" N THR A 395 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.964A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 478 through 486 removed outlier: 4.377A pdb=" N HIS A 482 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU A 495 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 484 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN A 493 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.405A pdb=" N VAL A 581 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 575 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 360 through 363 Processing sheet with id= H, first strand: chain 'B' and resid 389 through 392 Processing sheet with id= I, first strand: chain 'B' and resid 491 through 494 Processing sheet with id= J, first strand: chain 'B' and resid 348 through 353 removed outlier: 3.637A pdb=" N SER B 350 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 528 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS B 352 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 526 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 426 through 433 removed outlier: 3.924A pdb=" N GLU B 442 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 458 through 465 removed outlier: 3.643A pdb=" N LYS B 484 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 480 " --> pdb=" O MET B 463 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1308 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: 3.35 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1750 1.30 - 1.43: 3607 1.43 - 1.56: 6625 1.56 - 1.68: 19 1.68 - 1.81: 105 Bond restraints: 12106 Sorted by residual: bond pdb=" C27 NNM A1003 " pdb=" C28 NNM A1003 " ideal model delta sigma weight residual 1.577 1.344 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C18 NNM A1003 " pdb=" C19 NNM A1003 " ideal model delta sigma weight residual 1.332 1.561 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C7 NNM A1003 " pdb=" C8 NNM A1003 " ideal model delta sigma weight residual 1.547 1.329 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C38 NNM A1003 " pdb=" C39 NNM A1003 " ideal model delta sigma weight residual 1.327 1.544 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C12 NNM A1003 " pdb=" C13 NNM A1003 " ideal model delta sigma weight residual 1.569 1.355 0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 12101 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.62: 271 105.62 - 112.73: 6129 112.73 - 119.84: 4190 119.84 - 126.94: 5603 126.94 - 134.05: 239 Bond angle restraints: 16432 Sorted by residual: angle pdb=" C17 NNM A1003 " pdb=" C18 NNM A1003 " pdb=" C20 NNM A1003 " ideal model delta sigma weight residual 74.54 125.44 -50.90 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C12 NNM A1003 " pdb=" C13 NNM A1003 " pdb=" C15 NNM A1003 " ideal model delta sigma weight residual 74.49 120.29 -45.80 3.00e+00 1.11e-01 2.33e+02 angle pdb=" C22 NNM A1003 " pdb=" C23 NNM A1003 " pdb=" C25 NNM A1003 " ideal model delta sigma weight residual 74.54 120.18 -45.64 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C27 NNM A1003 " pdb=" C28 NNM A1003 " pdb=" C30 NNM A1003 " ideal model delta sigma weight residual 74.53 119.48 -44.95 3.00e+00 1.11e-01 2.25e+02 angle pdb=" C10 NNM A1003 " pdb=" C8 NNM A1003 " pdb=" C7 NNM A1003 " ideal model delta sigma weight residual 74.52 118.69 -44.17 3.00e+00 1.11e-01 2.17e+02 ... (remaining 16427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 6890 35.84 - 71.68: 97 71.68 - 107.52: 16 107.52 - 143.36: 1 143.36 - 179.20: 2 Dihedral angle restraints: 7006 sinusoidal: 2855 harmonic: 4151 Sorted by residual: dihedral pdb=" CA PRO A 712 " pdb=" C PRO A 712 " pdb=" N TRP A 713 " pdb=" CA TRP A 713 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TRP B 583 " pdb=" C TRP B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLY A 160 " pdb=" C GLY A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 7003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1481 0.077 - 0.154: 239 0.154 - 0.230: 25 0.230 - 0.307: 3 0.307 - 0.384: 2 Chirality restraints: 1750 Sorted by residual: chirality pdb=" CA ALA A 531 " pdb=" N ALA A 531 " pdb=" C ALA A 531 " pdb=" CB ALA A 531 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA PRO A 530 " pdb=" N PRO A 530 " pdb=" C PRO A 530 " pdb=" CB PRO A 530 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LEU A 584 " pdb=" N LEU A 584 " pdb=" C LEU A 584 " pdb=" CB LEU A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1747 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 654 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 655 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 729 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C TYR A 729 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR A 729 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 730 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 268 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C LEU B 268 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU B 268 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 269 " 0.017 2.00e-02 2.50e+03 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1585 2.76 - 3.29: 11299 3.29 - 3.83: 20396 3.83 - 4.36: 24445 4.36 - 4.90: 41492 Nonbonded interactions: 99217 Sorted by model distance: nonbonded pdb=" O LEU A 151 " pdb=" OG1 THR A 155 " model vdw 2.221 2.440 nonbonded pdb=" OE2 GLU B 93 " pdb=" OH TYR B 142 " model vdw 2.225 2.440 nonbonded pdb=" O PRO B 68 " pdb=" OG1 THR B 72 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 378 " pdb=" OE1 GLN B 506 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN A 580 " pdb=" OH TYR A 734 " model vdw 2.275 2.440 ... (remaining 99212 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.710 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 34.640 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.010 0.233 12106 Z= 0.615 Angle : 1.466 50.897 16432 Z= 0.638 Chirality : 0.057 0.384 1750 Planarity : 0.008 0.079 2030 Dihedral : 13.306 179.205 4343 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.40 % Allowed : 5.16 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.16), residues: 1414 helix: -3.20 (0.13), residues: 652 sheet: -2.90 (0.48), residues: 85 loop : -2.67 (0.19), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 727 HIS 0.018 0.002 HIS A 632 PHE 0.042 0.003 PHE B 301 TYR 0.044 0.003 TYR A 573 ARG 0.009 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 256 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8388 (pt) cc_final: 0.8060 (mt) REVERT: A 315 LYS cc_start: 0.8390 (mtpm) cc_final: 0.8150 (mtmt) REVERT: A 334 SER cc_start: 0.7784 (m) cc_final: 0.7426 (p) REVERT: A 340 THR cc_start: 0.8539 (m) cc_final: 0.8099 (p) REVERT: A 396 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7575 (pttm) REVERT: A 398 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6080 (ttm-80) REVERT: A 465 ASP cc_start: 0.7828 (t0) cc_final: 0.7611 (m-30) REVERT: A 471 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7756 (ttp-170) REVERT: A 529 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7096 (tptp) REVERT: A 546 HIS cc_start: 0.7705 (t70) cc_final: 0.7394 (t70) REVERT: A 610 SER cc_start: 0.8911 (t) cc_final: 0.8602 (p) REVERT: A 615 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6827 (mttt) REVERT: B 70 ILE cc_start: 0.8557 (mm) cc_final: 0.8338 (mt) REVERT: B 181 TRP cc_start: 0.8002 (m-10) cc_final: 0.7765 (m-10) REVERT: B 559 MET cc_start: 0.7373 (mtt) cc_final: 0.6889 (mtp) REVERT: B 560 MET cc_start: 0.7399 (mtp) cc_final: 0.6837 (mtp) REVERT: B 709 MET cc_start: 0.6910 (tpt) cc_final: 0.6519 (tpp) REVERT: B 738 PRO cc_start: 0.8218 (Cg_exo) cc_final: 0.7388 (Cg_endo) REVERT: B 753 ILE cc_start: 0.8556 (tt) cc_final: 0.7620 (tt) outliers start: 5 outliers final: 2 residues processed: 260 average time/residue: 0.2442 time to fit residues: 90.7283 Evaluate side-chains 162 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 713 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 30.0000 chunk 107 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 316 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS A 546 HIS B 106 HIS B 110 HIS B 221 HIS B 308 HIS B 327 GLN B 354 GLN B 465 GLN B 564 ASN B 635 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12106 Z= 0.285 Angle : 0.953 27.159 16432 Z= 0.403 Chirality : 0.042 0.145 1750 Planarity : 0.005 0.066 2030 Dihedral : 13.490 177.109 1753 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.14 % Allowed : 9.43 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.19), residues: 1414 helix: -1.09 (0.17), residues: 658 sheet: -2.79 (0.45), residues: 95 loop : -2.16 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 727 HIS 0.008 0.001 HIS A 632 PHE 0.025 0.002 PHE B 301 TYR 0.014 0.002 TYR B 602 ARG 0.005 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8410 (pt) cc_final: 0.8191 (mt) REVERT: A 214 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7888 (tm) REVERT: A 315 LYS cc_start: 0.8356 (mtpm) cc_final: 0.8102 (mtmt) REVERT: A 334 SER cc_start: 0.7716 (m) cc_final: 0.7233 (p) REVERT: A 340 THR cc_start: 0.8532 (m) cc_final: 0.7917 (p) REVERT: A 396 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7542 (pttm) REVERT: A 398 ARG cc_start: 0.6861 (mtt180) cc_final: 0.6247 (mtt90) REVERT: A 529 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7156 (tptp) REVERT: A 549 LYS cc_start: 0.7330 (ttpt) cc_final: 0.5906 (tppt) REVERT: A 588 ILE cc_start: 0.8301 (tt) cc_final: 0.7709 (mt) REVERT: A 615 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6857 (mttt) REVERT: B 277 MET cc_start: 0.9021 (ttm) cc_final: 0.8793 (ttm) REVERT: B 550 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6673 (mmtt) REVERT: B 560 MET cc_start: 0.7228 (mtp) cc_final: 0.6976 (mtm) REVERT: B 597 ASP cc_start: 0.7324 (m-30) cc_final: 0.7086 (m-30) REVERT: B 709 MET cc_start: 0.6924 (tpt) cc_final: 0.6722 (tpt) REVERT: B 748 PHE cc_start: 0.8046 (m-10) cc_final: 0.7751 (m-10) REVERT: B 753 ILE cc_start: 0.8648 (tt) cc_final: 0.8294 (tt) outliers start: 39 outliers final: 16 residues processed: 188 average time/residue: 0.2302 time to fit residues: 63.6900 Evaluate side-chains 160 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12106 Z= 0.250 Angle : 0.916 25.598 16432 Z= 0.379 Chirality : 0.041 0.144 1750 Planarity : 0.004 0.049 2030 Dihedral : 12.884 176.341 1749 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.38 % Allowed : 10.39 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1414 helix: -0.01 (0.19), residues: 671 sheet: -2.53 (0.47), residues: 94 loop : -1.85 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.021 0.002 PHE B 301 TYR 0.010 0.001 TYR A 344 ARG 0.004 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8412 (pt) cc_final: 0.8133 (mt) REVERT: A 214 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7991 (tm) REVERT: A 315 LYS cc_start: 0.8301 (mtpm) cc_final: 0.8041 (mtmt) REVERT: A 334 SER cc_start: 0.7913 (m) cc_final: 0.7292 (p) REVERT: A 396 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7490 (pttm) REVERT: A 398 ARG cc_start: 0.6754 (mtt180) cc_final: 0.6036 (mtt90) REVERT: A 400 PHE cc_start: 0.7713 (t80) cc_final: 0.7350 (t80) REVERT: A 409 HIS cc_start: 0.6442 (t70) cc_final: 0.6145 (t-90) REVERT: A 464 LEU cc_start: 0.8168 (mt) cc_final: 0.7816 (mt) REVERT: A 465 ASP cc_start: 0.7797 (t0) cc_final: 0.7352 (m-30) REVERT: A 529 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7196 (tptp) REVERT: A 549 LYS cc_start: 0.7387 (ttpt) cc_final: 0.5941 (tppt) REVERT: A 588 ILE cc_start: 0.8246 (tt) cc_final: 0.7886 (mt) REVERT: A 615 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6866 (mttt) REVERT: B 550 LYS cc_start: 0.7068 (mmtm) cc_final: 0.6692 (mmtt) REVERT: B 560 MET cc_start: 0.7213 (mtp) cc_final: 0.6952 (mtm) REVERT: B 597 ASP cc_start: 0.7387 (m-30) cc_final: 0.7146 (m-30) REVERT: B 699 LYS cc_start: 0.7496 (mttt) cc_final: 0.7225 (pttm) REVERT: B 709 MET cc_start: 0.7163 (tpt) cc_final: 0.6810 (tpt) REVERT: B 753 ILE cc_start: 0.8689 (tt) cc_final: 0.8374 (tt) outliers start: 42 outliers final: 20 residues processed: 183 average time/residue: 0.2239 time to fit residues: 60.4280 Evaluate side-chains 164 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 114 optimal weight: 10.0000 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12106 Z= 0.199 Angle : 0.886 24.519 16432 Z= 0.363 Chirality : 0.040 0.148 1750 Planarity : 0.004 0.048 2030 Dihedral : 12.478 175.788 1749 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.87 % Allowed : 10.48 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1414 helix: 0.56 (0.20), residues: 669 sheet: -2.37 (0.49), residues: 91 loop : -1.73 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 727 HIS 0.006 0.001 HIS A 632 PHE 0.017 0.001 PHE B 301 TYR 0.011 0.001 TYR A 344 ARG 0.003 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8388 (pt) cc_final: 0.8129 (mt) REVERT: A 193 MET cc_start: 0.8697 (mmm) cc_final: 0.8463 (mmm) REVERT: A 214 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8029 (tm) REVERT: A 315 LYS cc_start: 0.8355 (mtpm) cc_final: 0.8093 (mtmt) REVERT: A 329 ILE cc_start: 0.9243 (mt) cc_final: 0.9021 (tt) REVERT: A 398 ARG cc_start: 0.6730 (mtt180) cc_final: 0.5989 (mtt90) REVERT: A 409 HIS cc_start: 0.6292 (t70) cc_final: 0.5811 (t-90) REVERT: A 465 ASP cc_start: 0.7785 (t0) cc_final: 0.7303 (m-30) REVERT: A 529 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7261 (tptp) REVERT: A 549 LYS cc_start: 0.7469 (ttpt) cc_final: 0.6111 (tppt) REVERT: A 588 ILE cc_start: 0.8135 (tt) cc_final: 0.7894 (mt) REVERT: A 748 LYS cc_start: 0.7973 (mttp) cc_final: 0.7461 (mtpt) REVERT: B 550 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6742 (mmtt) REVERT: B 560 MET cc_start: 0.7238 (mtp) cc_final: 0.6972 (mtm) REVERT: B 597 ASP cc_start: 0.7285 (m-30) cc_final: 0.7027 (m-30) REVERT: B 605 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8017 (pt) REVERT: B 699 LYS cc_start: 0.7554 (mttt) cc_final: 0.7269 (pttm) REVERT: B 709 MET cc_start: 0.7200 (tpt) cc_final: 0.6762 (tpt) REVERT: B 753 ILE cc_start: 0.8724 (tt) cc_final: 0.8438 (tt) outliers start: 48 outliers final: 25 residues processed: 194 average time/residue: 0.2264 time to fit residues: 64.4645 Evaluate side-chains 170 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12106 Z= 0.212 Angle : 0.889 23.343 16432 Z= 0.362 Chirality : 0.041 0.209 1750 Planarity : 0.004 0.047 2030 Dihedral : 12.161 176.708 1749 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.55 % Allowed : 11.60 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1414 helix: 0.82 (0.20), residues: 669 sheet: -2.23 (0.50), residues: 91 loop : -1.59 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 727 HIS 0.006 0.001 HIS A 632 PHE 0.012 0.001 PHE A 121 TYR 0.009 0.001 TYR A 352 ARG 0.003 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8418 (pt) cc_final: 0.8150 (mt) REVERT: A 193 MET cc_start: 0.8658 (mmm) cc_final: 0.8444 (mmm) REVERT: A 214 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (tm) REVERT: A 315 LYS cc_start: 0.8370 (mtpm) cc_final: 0.8097 (mtmt) REVERT: A 398 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6211 (ttm170) REVERT: A 409 HIS cc_start: 0.6416 (t70) cc_final: 0.5866 (t-90) REVERT: A 465 ASP cc_start: 0.7820 (t0) cc_final: 0.7312 (m-30) REVERT: A 529 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7199 (tptp) REVERT: A 549 LYS cc_start: 0.7352 (ttpt) cc_final: 0.6052 (tppt) REVERT: A 748 LYS cc_start: 0.7972 (mttp) cc_final: 0.7467 (mtpt) REVERT: B 550 LYS cc_start: 0.7091 (mmtm) cc_final: 0.6759 (mmtt) REVERT: B 560 MET cc_start: 0.7269 (mtp) cc_final: 0.6993 (mtm) REVERT: B 597 ASP cc_start: 0.7351 (m-30) cc_final: 0.7086 (m-30) REVERT: B 611 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 650 MET cc_start: 0.8412 (tpp) cc_final: 0.8108 (tpp) REVERT: B 657 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8567 (tp) REVERT: B 699 LYS cc_start: 0.7711 (mttt) cc_final: 0.7367 (pttm) REVERT: B 709 MET cc_start: 0.7217 (tpt) cc_final: 0.6716 (tpt) REVERT: B 753 ILE cc_start: 0.8740 (tt) cc_final: 0.8469 (tt) outliers start: 44 outliers final: 29 residues processed: 185 average time/residue: 0.2332 time to fit residues: 62.9078 Evaluate side-chains 176 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12106 Z= 0.271 Angle : 0.905 22.851 16432 Z= 0.371 Chirality : 0.042 0.192 1750 Planarity : 0.004 0.049 2030 Dihedral : 12.024 177.512 1745 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.95 % Allowed : 12.57 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1414 helix: 0.90 (0.20), residues: 667 sheet: -2.13 (0.51), residues: 91 loop : -1.46 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.015 0.002 PHE A 121 TYR 0.011 0.001 TYR A 344 ARG 0.003 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8443 (pt) cc_final: 0.8127 (mt) REVERT: A 193 MET cc_start: 0.8699 (mmm) cc_final: 0.8448 (mmm) REVERT: A 214 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (tm) REVERT: A 315 LYS cc_start: 0.8312 (mtpm) cc_final: 0.8033 (mtmt) REVERT: A 398 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6199 (ttm170) REVERT: A 400 PHE cc_start: 0.7801 (t80) cc_final: 0.7398 (t80) REVERT: A 464 LEU cc_start: 0.8222 (mt) cc_final: 0.7889 (mt) REVERT: A 465 ASP cc_start: 0.7920 (t0) cc_final: 0.7403 (m-30) REVERT: A 529 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7190 (tptp) REVERT: A 549 LYS cc_start: 0.7356 (ttpt) cc_final: 0.6066 (tppt) REVERT: A 647 MET cc_start: 0.8805 (mtt) cc_final: 0.8598 (mtt) REVERT: A 748 LYS cc_start: 0.7973 (mttp) cc_final: 0.7467 (mtpt) REVERT: B 322 MET cc_start: 0.8293 (mmm) cc_final: 0.7600 (mmm) REVERT: B 550 LYS cc_start: 0.7067 (mmtm) cc_final: 0.6701 (mmtt) REVERT: B 560 MET cc_start: 0.7331 (mtp) cc_final: 0.7023 (mtm) REVERT: B 597 ASP cc_start: 0.7489 (m-30) cc_final: 0.7207 (m-30) REVERT: B 611 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8230 (m) REVERT: B 657 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8521 (tp) REVERT: B 699 LYS cc_start: 0.7705 (mttt) cc_final: 0.7368 (pttm) REVERT: B 709 MET cc_start: 0.7326 (tpt) cc_final: 0.6784 (tpt) REVERT: B 753 ILE cc_start: 0.8805 (tt) cc_final: 0.8501 (tt) outliers start: 49 outliers final: 33 residues processed: 173 average time/residue: 0.2289 time to fit residues: 58.0763 Evaluate side-chains 172 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 741 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12106 Z= 0.229 Angle : 0.892 22.734 16432 Z= 0.364 Chirality : 0.041 0.184 1750 Planarity : 0.004 0.049 2030 Dihedral : 11.878 177.905 1745 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.06 % Allowed : 13.22 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1414 helix: 1.03 (0.20), residues: 667 sheet: -2.10 (0.51), residues: 91 loop : -1.41 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.013 0.001 PHE A 121 TYR 0.010 0.001 TYR A 344 ARG 0.003 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8446 (pt) cc_final: 0.8142 (mt) REVERT: A 193 MET cc_start: 0.8696 (mmm) cc_final: 0.8457 (mmm) REVERT: A 214 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (tm) REVERT: A 315 LYS cc_start: 0.8305 (mtpm) cc_final: 0.8016 (mtmt) REVERT: A 396 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7738 (ttpt) REVERT: A 398 ARG cc_start: 0.6763 (mtt180) cc_final: 0.6160 (ttm170) REVERT: A 400 PHE cc_start: 0.7784 (t80) cc_final: 0.7424 (t80) REVERT: A 409 HIS cc_start: 0.5893 (t-90) cc_final: 0.5595 (t-90) REVERT: A 464 LEU cc_start: 0.8162 (mt) cc_final: 0.7810 (mt) REVERT: A 465 ASP cc_start: 0.7918 (t0) cc_final: 0.7353 (m-30) REVERT: A 529 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7181 (tptp) REVERT: A 549 LYS cc_start: 0.7157 (ttpt) cc_final: 0.5965 (tppt) REVERT: A 647 MET cc_start: 0.8773 (mtt) cc_final: 0.8562 (mtt) REVERT: A 748 LYS cc_start: 0.7989 (mttp) cc_final: 0.7482 (mtpt) REVERT: B 322 MET cc_start: 0.8316 (mmm) cc_final: 0.7673 (mmm) REVERT: B 550 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6735 (mmtt) REVERT: B 560 MET cc_start: 0.7330 (mtp) cc_final: 0.7021 (mtm) REVERT: B 597 ASP cc_start: 0.7496 (m-30) cc_final: 0.7210 (m-30) REVERT: B 611 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 657 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8555 (tp) REVERT: B 699 LYS cc_start: 0.7707 (mttt) cc_final: 0.7369 (pttm) REVERT: B 709 MET cc_start: 0.7318 (tpt) cc_final: 0.6768 (tpt) REVERT: B 753 ILE cc_start: 0.8768 (tt) cc_final: 0.8489 (tt) outliers start: 38 outliers final: 30 residues processed: 171 average time/residue: 0.2420 time to fit residues: 59.8663 Evaluate side-chains 169 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12106 Z= 0.163 Angle : 0.867 22.443 16432 Z= 0.349 Chirality : 0.040 0.162 1750 Planarity : 0.004 0.048 2030 Dihedral : 11.511 177.923 1745 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1414 helix: 1.27 (0.20), residues: 669 sheet: -2.10 (0.54), residues: 83 loop : -1.38 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 727 HIS 0.006 0.001 HIS A 632 PHE 0.013 0.001 PHE A 537 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8406 (pt) cc_final: 0.8122 (mt) REVERT: A 214 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (tm) REVERT: A 315 LYS cc_start: 0.8391 (mtpm) cc_final: 0.8085 (mtmt) REVERT: A 396 LYS cc_start: 0.7879 (ptpp) cc_final: 0.7674 (ttpt) REVERT: A 398 ARG cc_start: 0.6862 (mtt180) cc_final: 0.6287 (ttm170) REVERT: A 400 PHE cc_start: 0.7867 (t80) cc_final: 0.7513 (t80) REVERT: A 409 HIS cc_start: 0.5590 (t-90) cc_final: 0.4798 (t-90) REVERT: A 465 ASP cc_start: 0.7582 (t0) cc_final: 0.7019 (m-30) REVERT: A 474 MET cc_start: 0.7890 (mmp) cc_final: 0.7635 (mmm) REVERT: A 529 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7181 (tptp) REVERT: A 549 LYS cc_start: 0.6960 (ttpt) cc_final: 0.5895 (tppt) REVERT: A 709 TYR cc_start: 0.8836 (m-80) cc_final: 0.8578 (m-80) REVERT: B 119 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8903 (mtp) REVERT: B 322 MET cc_start: 0.8299 (mmm) cc_final: 0.7697 (mmm) REVERT: B 550 LYS cc_start: 0.7122 (mmtm) cc_final: 0.6772 (mmtt) REVERT: B 560 MET cc_start: 0.7358 (mtp) cc_final: 0.7060 (mtm) REVERT: B 597 ASP cc_start: 0.7474 (m-30) cc_final: 0.7162 (m-30) REVERT: B 611 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (m) REVERT: B 657 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8593 (tp) REVERT: B 699 LYS cc_start: 0.7693 (mttt) cc_final: 0.7380 (pttm) REVERT: B 709 MET cc_start: 0.7394 (tpt) cc_final: 0.6807 (tpt) REVERT: B 753 ILE cc_start: 0.8705 (tt) cc_final: 0.8502 (tt) outliers start: 34 outliers final: 23 residues processed: 169 average time/residue: 0.2270 time to fit residues: 56.1680 Evaluate side-chains 165 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12106 Z= 0.256 Angle : 0.896 22.466 16432 Z= 0.365 Chirality : 0.042 0.171 1750 Planarity : 0.004 0.049 2030 Dihedral : 11.593 178.506 1745 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.66 % Allowed : 14.02 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1414 helix: 1.23 (0.20), residues: 669 sheet: -2.28 (0.49), residues: 95 loop : -1.31 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.013 0.002 PHE A 121 TYR 0.010 0.001 TYR B 654 ARG 0.004 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8141 (tm) REVERT: A 271 PHE cc_start: 0.7443 (m-80) cc_final: 0.6058 (t80) REVERT: A 315 LYS cc_start: 0.8311 (mtpm) cc_final: 0.8016 (mtmt) REVERT: A 398 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6354 (ttm170) REVERT: A 400 PHE cc_start: 0.7723 (t80) cc_final: 0.7350 (t80) REVERT: A 409 HIS cc_start: 0.5854 (t-90) cc_final: 0.5477 (t-90) REVERT: A 465 ASP cc_start: 0.7922 (t0) cc_final: 0.7343 (m-30) REVERT: A 529 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7169 (tptp) REVERT: A 549 LYS cc_start: 0.7114 (ttpt) cc_final: 0.5991 (tppt) REVERT: A 709 TYR cc_start: 0.8938 (m-80) cc_final: 0.8606 (m-80) REVERT: B 119 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8953 (mtp) REVERT: B 550 LYS cc_start: 0.7083 (mmtm) cc_final: 0.6725 (mmtt) REVERT: B 560 MET cc_start: 0.7332 (mtp) cc_final: 0.7018 (mtm) REVERT: B 597 ASP cc_start: 0.7400 (m-30) cc_final: 0.7148 (m-30) REVERT: B 611 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 657 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 699 LYS cc_start: 0.7712 (mttt) cc_final: 0.7407 (pttm) REVERT: B 709 MET cc_start: 0.7493 (tpt) cc_final: 0.6859 (tpt) REVERT: B 753 ILE cc_start: 0.8802 (tt) cc_final: 0.8537 (tt) outliers start: 33 outliers final: 25 residues processed: 163 average time/residue: 0.2465 time to fit residues: 58.1085 Evaluate side-chains 162 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 0.0060 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 69 optimal weight: 0.0000 chunk 89 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12106 Z= 0.145 Angle : 0.868 22.379 16432 Z= 0.348 Chirality : 0.039 0.151 1750 Planarity : 0.004 0.048 2030 Dihedral : 11.248 179.321 1745 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.01 % Allowed : 14.75 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1414 helix: 1.49 (0.20), residues: 668 sheet: -2.25 (0.48), residues: 95 loop : -1.29 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 727 HIS 0.005 0.001 HIS A 632 PHE 0.013 0.001 PHE A 537 TYR 0.009 0.001 TYR A 352 ARG 0.007 0.000 ARG A 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8068 (tm) REVERT: A 315 LYS cc_start: 0.8384 (mtpm) cc_final: 0.8069 (mtmt) REVERT: A 398 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6171 (ttm170) REVERT: A 409 HIS cc_start: 0.5478 (t-90) cc_final: 0.4739 (t-90) REVERT: A 429 CYS cc_start: 0.8536 (m) cc_final: 0.7851 (t) REVERT: A 465 ASP cc_start: 0.7605 (t0) cc_final: 0.7045 (m-30) REVERT: A 529 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7144 (tptp) REVERT: A 549 LYS cc_start: 0.6836 (ttpt) cc_final: 0.5859 (tppt) REVERT: A 709 TYR cc_start: 0.8731 (m-80) cc_final: 0.8514 (m-80) REVERT: A 716 GLU cc_start: 0.7735 (tp30) cc_final: 0.7504 (pt0) REVERT: B 80 MET cc_start: 0.8227 (mpp) cc_final: 0.7833 (mtt) REVERT: B 119 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: B 550 LYS cc_start: 0.7125 (mmtm) cc_final: 0.6776 (mmtt) REVERT: B 560 MET cc_start: 0.7353 (mtp) cc_final: 0.7052 (mtm) REVERT: B 597 ASP cc_start: 0.7335 (m-30) cc_final: 0.7042 (m-30) REVERT: B 657 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 699 LYS cc_start: 0.7690 (mttt) cc_final: 0.7392 (pttm) REVERT: B 709 MET cc_start: 0.7474 (tpt) cc_final: 0.6841 (tpt) outliers start: 25 outliers final: 18 residues processed: 167 average time/residue: 0.2470 time to fit residues: 59.8749 Evaluate side-chains 162 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106935 restraints weight = 12990.106| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.89 r_work: 0.2887 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12106 Z= 0.280 Angle : 0.906 22.413 16432 Z= 0.372 Chirality : 0.042 0.170 1750 Planarity : 0.004 0.049 2030 Dihedral : 11.437 179.405 1745 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.18 % Allowed : 14.50 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1414 helix: 1.31 (0.20), residues: 669 sheet: -2.07 (0.51), residues: 84 loop : -1.24 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.021 0.002 PHE B 603 TYR 0.011 0.001 TYR B 654 ARG 0.007 0.000 ARG A 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.61 seconds wall clock time: 49 minutes 4.27 seconds (2944.27 seconds total)