Starting phenix.real_space_refine on Sun Apr 7 08:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syo_40886/04_2024/8syo_40886.pdb" } resolution = 2.94 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= 0.025 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6487 2.51 5 N 1695 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10069 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6474 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175} Chain: "C" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.69, per 1000 atoms: 0.57 Number of scatterers: 10069 At special positions: 0 Unit cell: (78.6176, 108.365, 172.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1825 8.00 N 1695 7.00 C 6487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 53.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.805A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.731A pdb=" N LEU A 218 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.628A pdb=" N ASP A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.647A pdb=" N ILE A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 310 through 323 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 350 through 365 removed outlier: 4.224A pdb=" N LYS A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.004A pdb=" N TRP A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.666A pdb=" N ASN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.666A pdb=" N GLU A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.885A pdb=" N LEU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.569A pdb=" N VAL A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.879A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.805A pdb=" N GLU A 540 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.689A pdb=" N PHE A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 removed outlier: 4.008A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.607A pdb=" N GLU A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.773A pdb=" N MET A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 667 through 689 Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.736A pdb=" N ALA A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 768 through 784 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.587A pdb=" N ARG A 819 " --> pdb=" O ASP A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 881 Processing helix chain 'A' and resid 883 through 901 Processing helix chain 'A' and resid 906 through 923 removed outlier: 3.633A pdb=" N HIS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.602A pdb=" N LYS B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.784A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.862A pdb=" N ALA C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.589A pdb=" N ARG B 180 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.530A pdb=" N LYS B 85 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE B 116 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 87 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 134 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 117 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.726A pdb=" N LEU C 177 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 272 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1761 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: 3.55 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3228 1.34 - 1.46: 1988 1.46 - 1.58: 4977 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10283 Sorted by residual: bond pdb=" CG1 ILE A 712 " pdb=" CD1 ILE A 712 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.09e+00 bond pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta sigma weight residual 1.463 1.478 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" C THR A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" SD MET A 395 " pdb=" CE MET A 395 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 10278 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.53: 185 105.53 - 112.64: 5561 112.64 - 119.76: 3273 119.76 - 126.87: 4782 126.87 - 133.98: 119 Bond angle restraints: 13920 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.45 115.92 -5.47 7.80e-01 1.64e+00 4.91e+01 angle pdb=" C ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 114.00 106.87 7.13 1.31e+00 5.83e-01 2.96e+01 angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CB LYS A 602 " pdb=" CG LYS A 602 " pdb=" CD LYS A 602 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB MET A 533 " pdb=" CG MET A 533 " pdb=" SD MET A 533 " ideal model delta sigma weight residual 112.70 102.95 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 13915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5653 17.65 - 35.31: 473 35.31 - 52.96: 67 52.96 - 70.61: 8 70.61 - 88.27: 9 Dihedral angle restraints: 6210 sinusoidal: 2513 harmonic: 3697 Sorted by residual: dihedral pdb=" CA CYS A 737 " pdb=" C CYS A 737 " pdb=" N LEU A 738 " pdb=" CA LEU A 738 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLY C 148 " pdb=" C GLY C 148 " pdb=" N LYS C 149 " pdb=" CA LYS C 149 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 535 " pdb=" C PRO A 535 " pdb=" N ASP A 536 " pdb=" CA ASP A 536 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1131 0.040 - 0.080: 318 0.080 - 0.120: 130 0.120 - 0.160: 23 0.160 - 0.199: 1 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA MET A 533 " pdb=" N MET A 533 " pdb=" C MET A 533 " pdb=" CB MET A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" C PRO A 535 " pdb=" CB PRO A 535 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1600 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO A 385 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 821 " -0.019 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR A 821 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 821 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 821 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 821 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 821 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 534 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 535 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.027 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 453 2.73 - 3.27: 10483 3.27 - 3.81: 16677 3.81 - 4.36: 19664 4.36 - 4.90: 33992 Nonbonded interactions: 81269 Sorted by model distance: nonbonded pdb=" NZ LYS B 25 " pdb=" O ASP B 174 " model vdw 2.182 2.520 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 2.520 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 2.520 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 2.440 ... (remaining 81264 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: 1.900 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: 0.000 Extract box with map and model: 5.820 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.190 Find NCS groups from input model: 0.270 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 0.069 10283 Z= 0.253 Angle : 0.625 9.753 13920 Z= 0.341 Chirality : 0.044 0.199 1603 Planarity : 0.005 0.083 1761 Dihedral : 13.189 88.268 3800 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.88 (0.25), residues: 1237 helix: 1.23 (0.21), residues: 597 sheet: 0.19 (0.38), residues: 197 loop : 0.04 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.014 0.001 HIS A 596 PHE 0.024 0.002 PHE C 93 TYR 0.041 0.002 TYR A 821 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.6920 (m-30) cc_final: 0.6653 (m-30) REVERT: A 123 GLU cc_start: 0.7404 (mp0) cc_final: 0.6884 (mp0) REVERT: A 344 MET cc_start: 0.8537 (mmt) cc_final: 0.8164 (mpp) REVERT: A 345 GLU cc_start: 0.7234 (pp20) cc_final: 0.6761 (pp20) REVERT: A 376 GLN cc_start: 0.6893 (tt0) cc_final: 0.6669 (mt0) REVERT: A 408 GLU cc_start: 0.7506 (tt0) cc_final: 0.6837 (tm-30) REVERT: A 416 GLU cc_start: 0.7041 (mp0) cc_final: 0.6501 (mp0) REVERT: A 420 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7784 (mtpm) REVERT: A 488 GLU cc_start: 0.7844 (tp30) cc_final: 0.7200 (tm-30) REVERT: A 567 GLU cc_start: 0.7564 (mp0) cc_final: 0.6937 (mp0) REVERT: A 590 MET cc_start: 0.8216 (mmm) cc_final: 0.8012 (mmm) REVERT: A 591 ASP cc_start: 0.7362 (m-30) cc_final: 0.7150 (m-30) REVERT: A 599 GLU cc_start: 0.7649 (pm20) cc_final: 0.7393 (pp20) REVERT: A 615 LYS cc_start: 0.8094 (tppt) cc_final: 0.7671 (tptp) REVERT: A 626 LEU cc_start: 0.8081 (tp) cc_final: 0.7878 (tt) REVERT: A 652 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7017 (tp-100) REVERT: A 655 SER cc_start: 0.8290 (m) cc_final: 0.7758 (p) REVERT: A 724 LEU cc_start: 0.8033 (mt) cc_final: 0.7798 (mt) REVERT: A 761 ILE cc_start: 0.8516 (mt) cc_final: 0.8112 (mt) REVERT: A 860 ASN cc_start: 0.7812 (t0) cc_final: 0.7554 (t0) REVERT: A 864 CYS cc_start: 0.7524 (m) cc_final: 0.7292 (m) REVERT: A 903 ASP cc_start: 0.7230 (t0) cc_final: 0.7021 (t0) REVERT: B 124 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6598 (tt0) REVERT: B 165 VAL cc_start: 0.8022 (m) cc_final: 0.7549 (p) REVERT: C 20 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 21 VAL cc_start: 0.8634 (t) cc_final: 0.8317 (p) REVERT: C 43 MET cc_start: 0.8870 (tmm) cc_final: 0.8319 (ttp) REVERT: C 50 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7966 (mm-40) REVERT: C 112 VAL cc_start: 0.8775 (p) cc_final: 0.8536 (t) REVERT: C 113 PHE cc_start: 0.8487 (m-10) cc_final: 0.8191 (m-10) REVERT: C 175 LYS cc_start: 0.8177 (mppt) cc_final: 0.7931 (mppt) REVERT: C 200 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 201 SER cc_start: 0.8473 (p) cc_final: 0.8247 (m) REVERT: C 231 GLU cc_start: 0.7537 (pt0) cc_final: 0.7240 (pt0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 1.2067 time to fit residues: 455.9931 Evaluate side-chains 283 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 673 GLN A 730 GLN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS B 72 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 70 GLN C 115 ASN C 117 GLN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10283 Z= 0.276 Angle : 0.622 10.061 13920 Z= 0.319 Chirality : 0.045 0.210 1603 Planarity : 0.005 0.060 1761 Dihedral : 4.259 19.275 1338 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.98 % Allowed : 13.72 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.20 (0.25), residues: 1237 helix: 1.48 (0.21), residues: 624 sheet: 0.51 (0.39), residues: 195 loop : 0.03 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.009 0.001 HIS A 789 PHE 0.022 0.002 PHE A 796 TYR 0.031 0.002 TYR B 73 ARG 0.007 0.001 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 291 time to evaluate : 1.131 Fit side-chains REVERT: A 123 GLU cc_start: 0.7297 (mp0) cc_final: 0.6722 (mp0) REVERT: A 344 MET cc_start: 0.8588 (mmt) cc_final: 0.8129 (mpp) REVERT: A 366 LYS cc_start: 0.8321 (ptpp) cc_final: 0.8000 (tppt) REVERT: A 416 GLU cc_start: 0.6955 (mp0) cc_final: 0.6528 (mp0) REVERT: A 419 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7796 (ttpp) REVERT: A 420 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7678 (mtpm) REVERT: A 488 GLU cc_start: 0.7781 (tp30) cc_final: 0.7401 (mm-30) REVERT: A 599 GLU cc_start: 0.7694 (pm20) cc_final: 0.7426 (pp20) REVERT: A 615 LYS cc_start: 0.7991 (tppt) cc_final: 0.7591 (tptp) REVERT: A 655 SER cc_start: 0.8181 (m) cc_final: 0.7837 (p) REVERT: A 730 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7146 (mt0) REVERT: A 870 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7756 (mm-40) REVERT: B 180 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7868 (mtp85) REVERT: C 20 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8302 (mt-10) REVERT: C 50 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7959 (mm-40) REVERT: C 112 VAL cc_start: 0.8863 (p) cc_final: 0.8582 (t) REVERT: C 113 PHE cc_start: 0.8545 (m-10) cc_final: 0.8277 (m-10) REVERT: C 173 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8543 (mp) REVERT: C 175 LYS cc_start: 0.8246 (mppt) cc_final: 0.7952 (mppt) REVERT: C 203 GLU cc_start: 0.7850 (tt0) cc_final: 0.7619 (tt0) REVERT: C 231 GLU cc_start: 0.7492 (pt0) cc_final: 0.7186 (pt0) outliers start: 45 outliers final: 16 residues processed: 311 average time/residue: 1.3031 time to fit residues: 434.3573 Evaluate side-chains 273 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 254 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 380 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 730 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10283 Z= 0.283 Angle : 0.643 12.391 13920 Z= 0.324 Chirality : 0.044 0.238 1603 Planarity : 0.004 0.052 1761 Dihedral : 4.334 19.926 1338 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.42 % Allowed : 18.14 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.29 (0.25), residues: 1237 helix: 1.59 (0.21), residues: 625 sheet: 0.60 (0.39), residues: 190 loop : -0.01 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 6 HIS 0.008 0.001 HIS B 128 PHE 0.030 0.002 PHE A 358 TYR 0.031 0.002 TYR B 73 ARG 0.007 0.000 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 268 time to evaluate : 1.287 Fit side-chains REVERT: A 22 LEU cc_start: 0.6482 (pp) cc_final: 0.6124 (mt) REVERT: A 123 GLU cc_start: 0.7340 (mp0) cc_final: 0.6752 (mp0) REVERT: A 344 MET cc_start: 0.8532 (mmt) cc_final: 0.8130 (tpp) REVERT: A 366 LYS cc_start: 0.8359 (ptpp) cc_final: 0.7924 (tppt) REVERT: A 395 MET cc_start: 0.7778 (mtt) cc_final: 0.7541 (mtp) REVERT: A 590 MET cc_start: 0.8204 (mmm) cc_final: 0.7750 (tpp) REVERT: A 595 LYS cc_start: 0.8473 (tmmt) cc_final: 0.8115 (tmmt) REVERT: A 599 GLU cc_start: 0.7706 (pm20) cc_final: 0.7442 (pp20) REVERT: A 615 LYS cc_start: 0.8021 (tppt) cc_final: 0.7610 (tptp) REVERT: A 652 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7399 (tp-100) REVERT: A 683 MET cc_start: 0.7776 (mmp) cc_final: 0.7549 (mmp) REVERT: A 689 MET cc_start: 0.7760 (mtp) cc_final: 0.7535 (ttm) REVERT: A 707 TYR cc_start: 0.7902 (t80) cc_final: 0.7681 (t80) REVERT: A 766 ARG cc_start: 0.7559 (tpp80) cc_final: 0.6999 (mtt90) REVERT: A 794 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 870 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7327 (mm-40) REVERT: A 873 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6870 (pp20) REVERT: B 158 ASP cc_start: 0.6179 (t70) cc_final: 0.5910 (t70) REVERT: B 165 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 180 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7846 (mtp85) REVERT: C 43 MET cc_start: 0.8783 (tmm) cc_final: 0.8551 (ttp) REVERT: C 50 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7932 (mm-40) REVERT: C 112 VAL cc_start: 0.8870 (p) cc_final: 0.8612 (t) REVERT: C 113 PHE cc_start: 0.8643 (m-10) cc_final: 0.8414 (m-10) REVERT: C 175 LYS cc_start: 0.8211 (mppt) cc_final: 0.7916 (mppt) REVERT: C 203 GLU cc_start: 0.7854 (tt0) cc_final: 0.7633 (tt0) REVERT: C 231 GLU cc_start: 0.7515 (pt0) cc_final: 0.7203 (pt0) REVERT: C 269 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8265 (mtmm) outliers start: 50 outliers final: 19 residues processed: 292 average time/residue: 1.2607 time to fit residues: 394.9084 Evaluate side-chains 272 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 250 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 376 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS B 130 ASN C 70 GLN C 115 ASN C 183 ASN C 233 GLN C 234 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10283 Z= 0.384 Angle : 0.669 11.533 13920 Z= 0.339 Chirality : 0.046 0.191 1603 Planarity : 0.005 0.050 1761 Dihedral : 4.577 19.372 1338 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.25 % Allowed : 19.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1237 helix: 1.49 (0.21), residues: 625 sheet: 0.55 (0.37), residues: 198 loop : -0.19 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 6 HIS 0.005 0.001 HIS B 128 PHE 0.013 0.002 PHE A 775 TYR 0.039 0.002 TYR B 73 ARG 0.008 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7366 (mp0) cc_final: 0.6955 (mt-10) REVERT: A 416 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6752 (mp0) REVERT: A 590 MET cc_start: 0.8246 (mmm) cc_final: 0.7856 (tpp) REVERT: A 595 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8219 (tttm) REVERT: A 599 GLU cc_start: 0.7798 (pm20) cc_final: 0.7579 (pp20) REVERT: A 615 LYS cc_start: 0.8034 (tppt) cc_final: 0.7621 (tptp) REVERT: A 643 MET cc_start: 0.8313 (mmt) cc_final: 0.7950 (mmm) REVERT: A 663 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7818 (tmm) REVERT: A 766 ARG cc_start: 0.7566 (tpp80) cc_final: 0.6907 (mtt90) REVERT: A 811 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6190 (tp30) REVERT: A 870 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7407 (mm-40) REVERT: B 89 ILE cc_start: 0.8026 (pt) cc_final: 0.7815 (pp) REVERT: B 122 LYS cc_start: 0.8250 (tmmt) cc_final: 0.8034 (tmmt) REVERT: B 165 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7698 (m) REVERT: C 43 MET cc_start: 0.8759 (tmm) cc_final: 0.8496 (ttp) REVERT: C 50 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7968 (mm-40) REVERT: C 112 VAL cc_start: 0.8903 (p) cc_final: 0.8672 (t) REVERT: C 113 PHE cc_start: 0.8695 (m-10) cc_final: 0.8234 (m-10) REVERT: C 175 LYS cc_start: 0.8266 (mppt) cc_final: 0.7993 (mppt) REVERT: C 203 GLU cc_start: 0.7871 (tt0) cc_final: 0.7646 (tt0) REVERT: C 231 GLU cc_start: 0.7529 (pt0) cc_final: 0.7234 (pt0) REVERT: C 269 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8251 (mtmm) outliers start: 48 outliers final: 22 residues processed: 292 average time/residue: 1.2533 time to fit residues: 391.9583 Evaluate side-chains 277 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 92 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10283 Z= 0.292 Angle : 0.646 11.778 13920 Z= 0.324 Chirality : 0.045 0.247 1603 Planarity : 0.004 0.045 1761 Dihedral : 4.463 19.712 1338 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.42 % Allowed : 22.65 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1237 helix: 1.63 (0.21), residues: 625 sheet: 0.43 (0.37), residues: 198 loop : -0.19 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 6 HIS 0.007 0.001 HIS B 90 PHE 0.033 0.002 PHE A 358 TYR 0.019 0.002 TYR B 73 ARG 0.008 0.000 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7370 (mp0) cc_final: 0.6945 (mt-10) REVERT: A 416 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6721 (mp0) REVERT: A 595 LYS cc_start: 0.8449 (tmmt) cc_final: 0.8227 (tttm) REVERT: A 599 GLU cc_start: 0.7770 (pm20) cc_final: 0.7491 (pp20) REVERT: A 615 LYS cc_start: 0.8023 (tppt) cc_final: 0.7628 (tptp) REVERT: A 643 MET cc_start: 0.8272 (mmt) cc_final: 0.8017 (mmm) REVERT: A 663 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7771 (tmm) REVERT: A 811 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6172 (tp30) REVERT: A 870 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7110 (mm-40) REVERT: A 873 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6826 (pp20) REVERT: A 888 SER cc_start: 0.8088 (t) cc_final: 0.7861 (p) REVERT: B 143 TYR cc_start: 0.8409 (p90) cc_final: 0.8065 (p90) REVERT: B 168 VAL cc_start: 0.8548 (p) cc_final: 0.8338 (m) REVERT: B 185 LYS cc_start: 0.7807 (ttpp) cc_final: 0.7544 (ttpt) REVERT: C 43 MET cc_start: 0.8754 (tmm) cc_final: 0.8505 (ttp) REVERT: C 50 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7990 (mm-40) REVERT: C 79 VAL cc_start: 0.9052 (t) cc_final: 0.8742 (m) REVERT: C 105 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8830 (OUTLIER) REVERT: C 112 VAL cc_start: 0.8886 (p) cc_final: 0.8658 (t) REVERT: C 113 PHE cc_start: 0.8685 (m-10) cc_final: 0.8291 (m-10) REVERT: C 175 LYS cc_start: 0.8281 (mppt) cc_final: 0.7983 (mppt) REVERT: C 231 GLU cc_start: 0.7541 (pt0) cc_final: 0.7251 (pt0) REVERT: C 269 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8257 (mtmm) outliers start: 50 outliers final: 21 residues processed: 287 average time/residue: 1.2688 time to fit residues: 390.3099 Evaluate side-chains 274 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 516 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS B 36 GLN B 128 HIS C 70 GLN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10283 Z= 0.231 Angle : 0.639 9.727 13920 Z= 0.320 Chirality : 0.044 0.207 1603 Planarity : 0.004 0.044 1761 Dihedral : 4.341 19.754 1338 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.07 % Allowed : 24.07 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.31 (0.25), residues: 1237 helix: 1.73 (0.21), residues: 626 sheet: 0.43 (0.37), residues: 200 loop : -0.14 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.016 0.001 PHE A 775 TYR 0.021 0.001 TYR B 73 ARG 0.009 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7357 (mp0) cc_final: 0.6923 (mt-10) REVERT: A 202 ASP cc_start: 0.7744 (t0) cc_final: 0.7369 (t0) REVERT: A 288 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7686 (ttt-90) REVERT: A 345 GLU cc_start: 0.7179 (pp20) cc_final: 0.6380 (pp20) REVERT: A 416 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6716 (mp0) REVERT: A 595 LYS cc_start: 0.8442 (tmmt) cc_final: 0.8073 (tmtt) REVERT: A 599 GLU cc_start: 0.7745 (pm20) cc_final: 0.7477 (pp20) REVERT: A 615 LYS cc_start: 0.8014 (tppt) cc_final: 0.7593 (tptp) REVERT: A 643 MET cc_start: 0.8302 (mmt) cc_final: 0.8046 (mmm) REVERT: A 794 VAL cc_start: 0.8556 (t) cc_final: 0.8331 (p) REVERT: A 811 GLU cc_start: 0.6368 (tm-30) cc_final: 0.6069 (tp30) REVERT: A 870 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7144 (mm-40) REVERT: A 873 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6850 (pp20) REVERT: A 888 SER cc_start: 0.8047 (t) cc_final: 0.7821 (p) REVERT: B 143 TYR cc_start: 0.8389 (p90) cc_final: 0.8068 (p90) REVERT: B 157 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: B 165 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7672 (m) REVERT: C 20 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 43 MET cc_start: 0.8776 (tmm) cc_final: 0.8553 (ttp) REVERT: C 50 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8035 (mm-40) REVERT: C 79 VAL cc_start: 0.9060 (t) cc_final: 0.8793 (m) REVERT: C 175 LYS cc_start: 0.8292 (mppt) cc_final: 0.7991 (mppt) REVERT: C 203 GLU cc_start: 0.7840 (tt0) cc_final: 0.7568 (tt0) REVERT: C 210 GLU cc_start: 0.8101 (pt0) cc_final: 0.7681 (pt0) REVERT: C 231 GLU cc_start: 0.7529 (pt0) cc_final: 0.7238 (pt0) outliers start: 46 outliers final: 20 residues processed: 287 average time/residue: 1.3146 time to fit residues: 404.4597 Evaluate side-chains 267 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 0.0060 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 4 HIS C 70 GLN C 115 ASN C 183 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 10283 Z= 0.290 Angle : 0.663 10.452 13920 Z= 0.328 Chirality : 0.045 0.268 1603 Planarity : 0.004 0.041 1761 Dihedral : 4.370 19.550 1338 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.89 % Allowed : 24.96 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.32 (0.25), residues: 1237 helix: 1.74 (0.21), residues: 627 sheet: 0.43 (0.37), residues: 200 loop : -0.14 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 6 HIS 0.008 0.001 HIS B 4 PHE 0.041 0.002 PHE A 358 TYR 0.024 0.002 TYR B 73 ARG 0.010 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7367 (mp0) cc_final: 0.6945 (mt-10) REVERT: A 248 ARG cc_start: 0.6839 (tmt-80) cc_final: 0.6461 (tpt90) REVERT: A 288 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7696 (ttt-90) REVERT: A 345 GLU cc_start: 0.7216 (pp20) cc_final: 0.6702 (pp20) REVERT: A 416 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6707 (mp0) REVERT: A 567 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 599 GLU cc_start: 0.7734 (pm20) cc_final: 0.7509 (pp20) REVERT: A 615 LYS cc_start: 0.8085 (tppt) cc_final: 0.7670 (tptp) REVERT: A 631 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: A 643 MET cc_start: 0.8306 (mmt) cc_final: 0.8029 (mmm) REVERT: A 663 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7743 (tmm) REVERT: A 722 LEU cc_start: 0.8659 (mt) cc_final: 0.8453 (tp) REVERT: A 811 GLU cc_start: 0.6340 (tm-30) cc_final: 0.6018 (tp30) REVERT: A 855 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7199 (mppt) REVERT: A 870 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7101 (mm-40) REVERT: A 873 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6834 (pp20) REVERT: A 888 SER cc_start: 0.8012 (t) cc_final: 0.7798 (p) REVERT: B 143 TYR cc_start: 0.8411 (p90) cc_final: 0.8057 (p90) REVERT: C 43 MET cc_start: 0.8773 (tmm) cc_final: 0.8572 (ttp) REVERT: C 50 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8032 (mm-40) REVERT: C 79 VAL cc_start: 0.9068 (t) cc_final: 0.8806 (m) REVERT: C 210 GLU cc_start: 0.8107 (pt0) cc_final: 0.7686 (pt0) outliers start: 44 outliers final: 24 residues processed: 279 average time/residue: 1.3369 time to fit residues: 398.3458 Evaluate side-chains 274 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 293 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS B 36 GLN C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10283 Z= 0.277 Angle : 0.662 10.811 13920 Z= 0.330 Chirality : 0.045 0.250 1603 Planarity : 0.004 0.041 1761 Dihedral : 4.339 19.601 1338 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.45 % Allowed : 26.02 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.35 (0.25), residues: 1237 helix: 1.76 (0.21), residues: 627 sheet: 0.42 (0.36), residues: 200 loop : -0.13 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 6 HIS 0.004 0.001 HIS A 826 PHE 0.035 0.002 PHE A 358 TYR 0.028 0.002 TYR B 73 ARG 0.010 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 260 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7500 (m90) cc_final: 0.7257 (m90) REVERT: A 123 GLU cc_start: 0.7367 (mp0) cc_final: 0.6953 (mt-10) REVERT: A 248 ARG cc_start: 0.6995 (tmt-80) cc_final: 0.6396 (tmt-80) REVERT: A 345 GLU cc_start: 0.7221 (pp20) cc_final: 0.6696 (pp20) REVERT: A 416 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6703 (mp0) REVERT: A 567 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 599 GLU cc_start: 0.7747 (pm20) cc_final: 0.7492 (pp20) REVERT: A 615 LYS cc_start: 0.8076 (tppt) cc_final: 0.7600 (tptp) REVERT: A 631 ARG cc_start: 0.7305 (mtt-85) cc_final: 0.6931 (mtt-85) REVERT: A 643 MET cc_start: 0.8298 (mmt) cc_final: 0.8035 (mmm) REVERT: A 663 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7700 (tmm) REVERT: A 722 LEU cc_start: 0.8647 (mt) cc_final: 0.8410 (tp) REVERT: A 811 GLU cc_start: 0.6373 (tm-30) cc_final: 0.6049 (tp30) REVERT: A 855 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7333 (mppt) REVERT: A 859 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6606 (pm20) REVERT: A 870 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7174 (mm-40) REVERT: A 888 SER cc_start: 0.7986 (t) cc_final: 0.7773 (p) REVERT: B 143 TYR cc_start: 0.8406 (p90) cc_final: 0.8073 (p90) REVERT: C 13 ASN cc_start: 0.8633 (p0) cc_final: 0.8412 (p0) REVERT: C 43 MET cc_start: 0.8763 (tmm) cc_final: 0.8547 (ttp) REVERT: C 50 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8011 (mm-40) REVERT: C 79 VAL cc_start: 0.9066 (t) cc_final: 0.8835 (m) outliers start: 39 outliers final: 21 residues processed: 279 average time/residue: 1.3407 time to fit residues: 399.9115 Evaluate side-chains 274 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 293 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 10283 Z= 0.299 Angle : 0.698 11.773 13920 Z= 0.350 Chirality : 0.046 0.235 1603 Planarity : 0.004 0.042 1761 Dihedral : 4.365 19.737 1338 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.19 % Allowed : 26.90 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.30 (0.25), residues: 1237 helix: 1.69 (0.21), residues: 625 sheet: 0.40 (0.37), residues: 200 loop : -0.07 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 6 HIS 0.004 0.001 HIS A 826 PHE 0.015 0.002 PHE B 84 TYR 0.032 0.002 TYR B 73 ARG 0.010 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7519 (m90) cc_final: 0.7318 (m90) REVERT: A 248 ARG cc_start: 0.7027 (tmt-80) cc_final: 0.6667 (tmt-80) REVERT: A 345 GLU cc_start: 0.7226 (pp20) cc_final: 0.6697 (pp20) REVERT: A 416 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6714 (mp0) REVERT: A 567 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 599 GLU cc_start: 0.7749 (pm20) cc_final: 0.7493 (pp20) REVERT: A 615 LYS cc_start: 0.8072 (tppt) cc_final: 0.7614 (tptp) REVERT: A 631 ARG cc_start: 0.7346 (mtt-85) cc_final: 0.6917 (mtt-85) REVERT: A 643 MET cc_start: 0.8294 (mmt) cc_final: 0.8042 (mmm) REVERT: A 663 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: A 811 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6084 (tp30) REVERT: A 855 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7370 (mppt) REVERT: A 870 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6971 (mm-40) REVERT: A 873 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6765 (pp20) REVERT: A 888 SER cc_start: 0.7991 (t) cc_final: 0.7777 (p) REVERT: B 4 HIS cc_start: 0.6457 (m170) cc_final: 0.5936 (m170) REVERT: B 143 TYR cc_start: 0.8398 (p90) cc_final: 0.8108 (p90) REVERT: C 13 ASN cc_start: 0.8637 (p0) cc_final: 0.8399 (p0) REVERT: C 43 MET cc_start: 0.8769 (tmm) cc_final: 0.8515 (ttp) REVERT: C 79 VAL cc_start: 0.9054 (t) cc_final: 0.8829 (m) outliers start: 36 outliers final: 22 residues processed: 276 average time/residue: 1.3070 time to fit residues: 385.3961 Evaluate side-chains 278 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 293 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.0270 chunk 124 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 99 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 596 HIS A 666 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10283 Z= 0.249 Angle : 0.719 13.622 13920 Z= 0.356 Chirality : 0.045 0.238 1603 Planarity : 0.005 0.046 1761 Dihedral : 4.360 19.780 1338 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.30 % Allowed : 28.05 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.31 (0.25), residues: 1237 helix: 1.69 (0.21), residues: 627 sheet: 0.50 (0.37), residues: 195 loop : -0.12 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.005 0.001 HIS B 128 PHE 0.045 0.002 PHE A 358 TYR 0.027 0.002 TYR B 73 ARG 0.008 0.001 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 1.180 Fit side-chains REVERT: A 7 HIS cc_start: 0.7507 (m90) cc_final: 0.7220 (m90) REVERT: A 248 ARG cc_start: 0.7038 (tmt-80) cc_final: 0.6698 (tmt-80) REVERT: A 288 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7681 (ttt-90) REVERT: A 345 GLU cc_start: 0.7244 (pp20) cc_final: 0.6734 (pp20) REVERT: A 416 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6709 (mp0) REVERT: A 567 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 595 LYS cc_start: 0.8361 (tmmt) cc_final: 0.8153 (tttm) REVERT: A 599 GLU cc_start: 0.7741 (pm20) cc_final: 0.7522 (pp20) REVERT: A 615 LYS cc_start: 0.8046 (tppt) cc_final: 0.7588 (tptp) REVERT: A 631 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.6898 (mtt-85) REVERT: A 643 MET cc_start: 0.8299 (mmt) cc_final: 0.8044 (mmm) REVERT: A 663 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: A 766 ARG cc_start: 0.7360 (tpp80) cc_final: 0.7151 (tpp80) REVERT: A 811 GLU cc_start: 0.6370 (tm-30) cc_final: 0.6036 (tp30) REVERT: A 855 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7459 (mppt) REVERT: A 859 GLU cc_start: 0.6782 (mp0) cc_final: 0.6530 (pm20) REVERT: A 870 GLN cc_start: 0.7344 (mm-40) cc_final: 0.6821 (mm-40) REVERT: A 873 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6788 (pp20) REVERT: A 888 SER cc_start: 0.7951 (t) cc_final: 0.7743 (p) REVERT: B 143 TYR cc_start: 0.8383 (p90) cc_final: 0.8061 (p90) REVERT: C 13 ASN cc_start: 0.8613 (p0) cc_final: 0.8373 (p0) REVERT: C 43 MET cc_start: 0.8741 (tmm) cc_final: 0.8512 (ttp) REVERT: C 79 VAL cc_start: 0.9059 (t) cc_final: 0.8838 (m) outliers start: 26 outliers final: 17 residues processed: 274 average time/residue: 1.3539 time to fit residues: 397.9285 Evaluate side-chains 275 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120079 restraints weight = 17384.143| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.45 r_work: 0.3566 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 10283 Z= 0.321 Angle : 0.728 15.468 13920 Z= 0.361 Chirality : 0.046 0.223 1603 Planarity : 0.005 0.047 1761 Dihedral : 4.439 19.560 1338 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.48 % Allowed : 27.88 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1237 helix: 1.63 (0.21), residues: 625 sheet: 0.34 (0.36), residues: 200 loop : -0.10 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 490 HIS 0.007 0.001 HIS B 37 PHE 0.044 0.002 PHE A 358 TYR 0.029 0.002 TYR B 73 ARG 0.009 0.001 ARG A 819 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.35 seconds wall clock time: 100 minutes 51.56 seconds (6051.56 seconds total)