Starting phenix.real_space_refine on Sat Nov 16 01:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/11_2024/8syn_40885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/11_2024/8syn_40885.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/8syn_40885/11_2024/8syn_40885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/11_2024/8syn_40885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/11_2024/8syn_40885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/11_2024/8syn_40885.cif" } 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= 0.018 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. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.11, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 2.80 Conformation dependent library (CDL) restraints added in 1.2 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: 1.14 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: 3.52 Time building geometry restraints manager: 3.16 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: 0.00 - 1.95: 13658 1.95 - 3.90: 222 3.90 - 5.85: 34 5.85 - 7.80: 4 7.80 - 9.75: 2 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 3.120 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 3.120 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 3.120 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.760 Find NCS groups from input model: 0.080 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:11.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7396 (tttt) cc_final: 0.7129 (tttp) REVERT: A 344 MET cc_start: 0.8505 (mmt) cc_final: 0.8076 (mpp) REVERT: A 366 LYS cc_start: 0.7729 (tptp) cc_final: 0.7400 (tppt) REVERT: A 488 GLU cc_start: 0.7811 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 514 CYS cc_start: 0.7977 (m) cc_final: 0.7600 (m) REVERT: A 584 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 595 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8215 (tmmm) REVERT: A 599 GLU cc_start: 0.7619 (pm20) cc_final: 0.7386 (mp0) REVERT: A 630 LYS cc_start: 0.7670 (mttp) cc_final: 0.7330 (mtmm) REVERT: A 659 GLU cc_start: 0.6575 (pp20) cc_final: 0.6102 (tm-30) REVERT: A 868 MET cc_start: 0.5468 (mtm) cc_final: 0.4972 (mtm) REVERT: B 43 ASN cc_start: 0.7578 (m110) cc_final: 0.7253 (m110) REVERT: C 14 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8299 (mtmt) REVERT: C 44 GLU cc_start: 0.8046 (tt0) cc_final: 0.7820 (tt0) REVERT: C 175 LYS cc_start: 0.8205 (mppt) cc_final: 0.7831 (mppt) REVERT: C 176 PHE cc_start: 0.7972 (p90) cc_final: 0.7755 (p90) REVERT: C 231 GLU cc_start: 0.7546 (pt0) cc_final: 0.7304 (pt0) REVERT: C 269 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7895 (mtmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 1.2434 time to fit residues: 353.5999 Evaluate side-chains 238 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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: 0.5980 chunk 94 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 59 optimal weight: 0.0570 chunk 72 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS A 778 ASN C 115 ASN C 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10283 Z= 0.210 Angle : 0.604 8.179 13920 Z= 0.309 Chirality : 0.044 0.144 1603 Planarity : 0.004 0.061 1761 Dihedral : 4.269 19.212 1338 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % 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: 1.60 (0.21), residues: 624 sheet: 0.48 (0.39), residues: 197 loop : 0.05 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 810 HIS 0.009 0.001 HIS B 90 PHE 0.025 0.002 PHE A 796 TYR 0.028 0.002 TYR B 73 ARG 0.006 0.000 ARG A 819 *********************** 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 269 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7610 (t0) cc_final: 0.7352 (t0) REVERT: A 344 MET cc_start: 0.8516 (mmt) cc_final: 0.8067 (tpp) REVERT: A 366 LYS cc_start: 0.7792 (tptp) cc_final: 0.7448 (tppt) REVERT: A 395 MET cc_start: 0.7873 (mtt) cc_final: 0.7603 (mtp) REVERT: A 419 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7552 (ttmt) REVERT: A 488 GLU cc_start: 0.7676 (tp30) cc_final: 0.7383 (mm-30) REVERT: A 514 CYS cc_start: 0.8032 (m) cc_final: 0.7614 (m) REVERT: A 551 LYS cc_start: 0.7447 (mttm) cc_final: 0.7175 (mttm) REVERT: A 584 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6514 (tm-30) REVERT: A 595 LYS cc_start: 0.8470 (tmmt) cc_final: 0.7929 (tmmm) REVERT: A 596 HIS cc_start: 0.7992 (m170) cc_final: 0.7624 (m-70) REVERT: A 630 LYS cc_start: 0.7640 (mttp) cc_final: 0.7340 (mtmm) REVERT: A 652 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6935 (tp-100) REVERT: A 659 GLU cc_start: 0.6552 (pp20) cc_final: 0.6125 (tm-30) REVERT: A 661 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7542 (ttm110) REVERT: A 666 ASN cc_start: 0.7167 (t0) cc_final: 0.6943 (t0) REVERT: A 868 MET cc_start: 0.5498 (mtm) cc_final: 0.4983 (mtm) REVERT: B 12 ASP cc_start: 0.8211 (m-30) cc_final: 0.8000 (m-30) REVERT: B 176 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7966 (m) REVERT: C 13 ASN cc_start: 0.8428 (p0) cc_final: 0.8216 (p0) REVERT: C 14 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8308 (mtmt) REVERT: C 43 MET cc_start: 0.8375 (tmm) cc_final: 0.8091 (ttm) REVERT: C 44 GLU cc_start: 0.8022 (tt0) cc_final: 0.7795 (tt0) REVERT: C 175 LYS cc_start: 0.8228 (mppt) cc_final: 0.7842 (mppt) REVERT: C 231 GLU cc_start: 0.7449 (pt0) cc_final: 0.7223 (pt0) REVERT: C 269 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7947 (mtmm) REVERT: C 290 PHE cc_start: 0.8361 (m-80) cc_final: 0.8130 (m-80) outliers start: 19 outliers final: 8 residues processed: 258 average time/residue: 1.0950 time to fit residues: 306.1307 Evaluate side-chains 241 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.0010 chunk 77 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 186 ASN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10283 Z= 0.261 Angle : 0.594 8.443 13920 Z= 0.303 Chirality : 0.044 0.152 1603 Planarity : 0.004 0.053 1761 Dihedral : 4.235 18.638 1338 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.30 % Allowed : 13.01 % Favored : 84.69 % 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: 1.39 (0.25), residues: 1237 helix: 1.70 (0.21), residues: 628 sheet: 0.43 (0.39), residues: 197 loop : 0.08 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.006 0.001 HIS B 90 PHE 0.037 0.002 PHE A 796 TYR 0.029 0.002 TYR B 73 ARG 0.009 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 271 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.6377 (tm-30) cc_final: 0.6144 (tm-30) REVERT: A 366 LYS cc_start: 0.7798 (tptp) cc_final: 0.7452 (tppt) REVERT: A 375 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7318 (m-40) REVERT: A 419 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7525 (ttmp) REVERT: A 488 GLU cc_start: 0.7784 (tp30) cc_final: 0.7482 (mm-30) REVERT: A 551 LYS cc_start: 0.7514 (mttm) cc_final: 0.7249 (mttm) REVERT: A 574 ASP cc_start: 0.7443 (t70) cc_final: 0.7242 (t0) REVERT: A 584 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6459 (tm-30) REVERT: A 595 LYS cc_start: 0.8502 (tmmt) cc_final: 0.8015 (tmmm) REVERT: A 596 HIS cc_start: 0.7967 (m170) cc_final: 0.7489 (m-70) REVERT: A 599 GLU cc_start: 0.7689 (pm20) cc_final: 0.7462 (mp0) REVERT: A 630 LYS cc_start: 0.7675 (mttp) cc_final: 0.7344 (mtmm) REVERT: A 659 GLU cc_start: 0.6608 (pp20) cc_final: 0.6228 (tm-30) REVERT: A 666 ASN cc_start: 0.7238 (t0) cc_final: 0.6954 (t0) REVERT: A 868 MET cc_start: 0.5521 (mtm) cc_final: 0.5004 (mtm) REVERT: C 14 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8403 (mtmt) REVERT: C 43 MET cc_start: 0.8334 (tmm) cc_final: 0.8059 (ttm) REVERT: C 44 GLU cc_start: 0.8045 (tt0) cc_final: 0.7780 (tt0) REVERT: C 175 LYS cc_start: 0.8206 (mppt) cc_final: 0.7829 (mppt) REVERT: C 176 PHE cc_start: 0.8198 (p90) cc_final: 0.7924 (p90) REVERT: C 231 GLU cc_start: 0.7460 (pt0) cc_final: 0.7235 (pt0) REVERT: C 269 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7936 (mtmm) outliers start: 26 outliers final: 13 residues processed: 255 average time/residue: 1.1652 time to fit residues: 320.3076 Evaluate side-chains 246 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 608 ASN A 727 HIS A 911 GLN C 115 ASN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10283 Z= 0.255 Angle : 0.603 12.933 13920 Z= 0.306 Chirality : 0.044 0.172 1603 Planarity : 0.004 0.049 1761 Dihedral : 4.224 19.365 1338 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.21 % Allowed : 15.66 % Favored : 82.12 % 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: 1.46 (0.25), residues: 1237 helix: 1.77 (0.21), residues: 627 sheet: 0.41 (0.39), residues: 199 loop : 0.13 (0.33), 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 0.043 0.002 PHE A 796 TYR 0.022 0.002 TYR B 143 ARG 0.006 0.000 ARG A 686 *********************** 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 263 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 352 GLU cc_start: 0.6495 (tm-30) cc_final: 0.6210 (tm-30) REVERT: A 366 LYS cc_start: 0.7800 (tptp) cc_final: 0.7455 (tppt) REVERT: A 416 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 419 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7607 (ttmt) REVERT: A 488 GLU cc_start: 0.7794 (tp30) cc_final: 0.7505 (mm-30) REVERT: A 551 LYS cc_start: 0.7543 (mttm) cc_final: 0.7284 (mttm) REVERT: A 567 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7419 (mp0) REVERT: A 574 ASP cc_start: 0.7466 (t70) cc_final: 0.7250 (t0) REVERT: A 584 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6431 (tm-30) REVERT: A 590 MET cc_start: 0.8107 (mmm) cc_final: 0.7745 (tpt) REVERT: A 595 LYS cc_start: 0.8509 (tmmt) cc_final: 0.7787 (tmmm) REVERT: A 599 GLU cc_start: 0.7678 (pm20) cc_final: 0.7388 (mp0) REVERT: A 630 LYS cc_start: 0.7687 (mttp) cc_final: 0.7345 (mtmm) REVERT: A 637 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (mp) REVERT: A 659 GLU cc_start: 0.6711 (pp20) cc_final: 0.6312 (tm-30) REVERT: A 661 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7414 (ttm110) REVERT: A 666 ASN cc_start: 0.7240 (t0) cc_final: 0.6904 (t0) REVERT: A 686 ARG cc_start: 0.6397 (tmm160) cc_final: 0.6119 (tmm160) REVERT: A 708 CYS cc_start: 0.7343 (p) cc_final: 0.7060 (t) REVERT: A 712 ILE cc_start: 0.8176 (mp) cc_final: 0.7909 (mp) REVERT: A 771 PHE cc_start: 0.8365 (m-80) cc_final: 0.8118 (m-80) REVERT: A 800 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: A 868 MET cc_start: 0.5508 (mtm) cc_final: 0.4983 (mtm) REVERT: C 14 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8405 (mtmt) REVERT: C 44 GLU cc_start: 0.8044 (tt0) cc_final: 0.7766 (tt0) REVERT: C 95 PHE cc_start: 0.8269 (m-80) cc_final: 0.7998 (m-80) REVERT: C 175 LYS cc_start: 0.8199 (mppt) cc_final: 0.7817 (mppt) REVERT: C 176 PHE cc_start: 0.8205 (p90) cc_final: 0.7958 (p90) REVERT: C 231 GLU cc_start: 0.7455 (pt0) cc_final: 0.7236 (pt0) REVERT: C 269 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7922 (mtmm) REVERT: C 290 PHE cc_start: 0.8360 (m-80) cc_final: 0.8113 (m-80) outliers start: 25 outliers final: 11 residues processed: 244 average time/residue: 1.2043 time to fit residues: 316.1054 Evaluate side-chains 248 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS B 170 GLN C 115 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10283 Z= 0.289 Angle : 0.604 10.038 13920 Z= 0.307 Chirality : 0.044 0.153 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.260 18.507 1338 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.83 % Allowed : 16.11 % Favored : 81.06 % 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: 1.43 (0.25), residues: 1237 helix: 1.75 (0.21), residues: 627 sheet: 0.35 (0.39), residues: 199 loop : 0.15 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 490 HIS 0.006 0.001 HIS A 596 PHE 0.032 0.002 PHE A 796 TYR 0.023 0.002 TYR B 143 ARG 0.007 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 270 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7933 (t) cc_final: 0.7626 (t) REVERT: A 202 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7311 (t0) REVERT: A 352 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6255 (tm-30) REVERT: A 366 LYS cc_start: 0.7798 (tptp) cc_final: 0.7461 (tppt) REVERT: A 416 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6858 (mp0) REVERT: A 419 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7605 (ttmt) REVERT: A 488 GLU cc_start: 0.7893 (tp30) cc_final: 0.7593 (mm-30) REVERT: A 551 LYS cc_start: 0.7578 (mttm) cc_final: 0.7319 (mttm) REVERT: A 567 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 574 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 584 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6431 (tm-30) REVERT: A 590 MET cc_start: 0.8085 (mmm) cc_final: 0.7686 (tpt) REVERT: A 595 LYS cc_start: 0.8558 (tmmt) cc_final: 0.8044 (tttm) REVERT: A 630 LYS cc_start: 0.7713 (mttp) cc_final: 0.7362 (mtmm) REVERT: A 632 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: A 637 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 659 GLU cc_start: 0.6813 (pp20) cc_final: 0.6377 (tm-30) REVERT: A 661 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7458 (ttm110) REVERT: A 666 ASN cc_start: 0.7269 (t0) cc_final: 0.6924 (t0) REVERT: A 686 ARG cc_start: 0.6468 (tmm160) cc_final: 0.6264 (tmm160) REVERT: A 708 CYS cc_start: 0.7321 (p) cc_final: 0.7103 (t) REVERT: A 712 ILE cc_start: 0.8156 (mp) cc_final: 0.7819 (mp) REVERT: A 868 MET cc_start: 0.5526 (mtm) cc_final: 0.5001 (mtm) REVERT: C 14 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8441 (mtmt) REVERT: C 43 MET cc_start: 0.8374 (tmm) cc_final: 0.8135 (ttm) REVERT: C 44 GLU cc_start: 0.8065 (tt0) cc_final: 0.7826 (tt0) REVERT: C 95 PHE cc_start: 0.8280 (m-80) cc_final: 0.8008 (m-80) REVERT: C 175 LYS cc_start: 0.8197 (mppt) cc_final: 0.7934 (mppt) REVERT: C 176 PHE cc_start: 0.8263 (p90) cc_final: 0.7918 (p90) REVERT: C 203 GLU cc_start: 0.7431 (tt0) cc_final: 0.6832 (tt0) REVERT: C 269 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7940 (mtmm) REVERT: C 290 PHE cc_start: 0.8351 (m-80) cc_final: 0.8105 (m-80) outliers start: 32 outliers final: 15 residues processed: 248 average time/residue: 1.2653 time to fit residues: 338.1238 Evaluate side-chains 254 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 534 THR 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 637 ILE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.0050 chunk 116 optimal weight: 0.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN A 516 HIS A 727 HIS C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10283 Z= 0.220 Angle : 0.600 10.497 13920 Z= 0.302 Chirality : 0.043 0.158 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.243 18.000 1338 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.48 % Allowed : 18.05 % Favored : 79.47 % 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: 1.55 (0.25), residues: 1237 helix: 1.86 (0.21), residues: 625 sheet: 0.38 (0.39), residues: 199 loop : 0.20 (0.33), residues: 413 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 0.026 0.001 PHE B 132 TYR 0.022 0.002 TYR B 143 ARG 0.006 0.000 ARG A 121 *********************** 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 268 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7866 (t) cc_final: 0.7556 (t) REVERT: A 352 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6205 (tm-30) REVERT: A 366 LYS cc_start: 0.7802 (tptp) cc_final: 0.7456 (tppt) REVERT: A 416 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6883 (mm-30) REVERT: A 419 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7595 (ttmt) REVERT: A 488 GLU cc_start: 0.7864 (tp30) cc_final: 0.7569 (mm-30) REVERT: A 551 LYS cc_start: 0.7572 (mttm) cc_final: 0.7301 (mttm) REVERT: A 574 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7252 (t0) REVERT: A 584 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6391 (tm-30) REVERT: A 590 MET cc_start: 0.8091 (mmm) cc_final: 0.7714 (tpt) REVERT: A 595 LYS cc_start: 0.8488 (tmmt) cc_final: 0.7755 (tppp) REVERT: A 630 LYS cc_start: 0.7699 (mttp) cc_final: 0.7260 (mtmm) REVERT: A 637 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 659 GLU cc_start: 0.6830 (pp20) cc_final: 0.6455 (tm-30) REVERT: A 666 ASN cc_start: 0.7190 (t0) cc_final: 0.6840 (t0) REVERT: A 771 PHE cc_start: 0.8324 (m-80) cc_final: 0.8095 (m-80) REVERT: A 868 MET cc_start: 0.5523 (mtm) cc_final: 0.4997 (mtm) REVERT: C 14 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8385 (mtmt) REVERT: C 43 MET cc_start: 0.8381 (tmm) cc_final: 0.8180 (ttm) REVERT: C 44 GLU cc_start: 0.8060 (tt0) cc_final: 0.7827 (tt0) REVERT: C 95 PHE cc_start: 0.8219 (m-80) cc_final: 0.7844 (m-80) REVERT: C 176 PHE cc_start: 0.8260 (p90) cc_final: 0.7930 (p90) REVERT: C 269 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7914 (mtmm) REVERT: C 290 PHE cc_start: 0.8342 (m-80) cc_final: 0.8121 (m-80) outliers start: 28 outliers final: 16 residues processed: 249 average time/residue: 1.2208 time to fit residues: 327.0012 Evaluate side-chains 256 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN 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: 0.0030 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS A 730 GLN C 115 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10283 Z= 0.244 Angle : 0.619 9.908 13920 Z= 0.311 Chirality : 0.044 0.150 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.224 20.294 1338 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.36 % Allowed : 17.79 % Favored : 78.85 % 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: 1.54 (0.25), residues: 1237 helix: 1.87 (0.21), residues: 625 sheet: 0.38 (0.39), residues: 199 loop : 0.15 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.005 0.001 HIS B 90 PHE 0.023 0.002 PHE A 796 TYR 0.024 0.002 TYR B 143 ARG 0.007 0.000 ARG A 121 *********************** 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 281 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.7872 (t) cc_final: 0.7566 (t) REVERT: A 202 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7270 (t0) REVERT: A 248 ARG cc_start: 0.7034 (tpt90) cc_final: 0.6729 (tpt90) REVERT: A 352 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6205 (tm-30) REVERT: A 395 MET cc_start: 0.7768 (mtt) cc_final: 0.7565 (mtp) REVERT: A 416 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7109 (mm-30) REVERT: A 419 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7583 (ttmt) REVERT: A 488 GLU cc_start: 0.7882 (tp30) cc_final: 0.7564 (mm-30) REVERT: A 551 LYS cc_start: 0.7587 (mttm) cc_final: 0.7313 (mttm) REVERT: A 567 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7693 (mp0) REVERT: A 584 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6379 (tm-30) REVERT: A 590 MET cc_start: 0.8089 (mmm) cc_final: 0.7736 (tpt) REVERT: A 595 LYS cc_start: 0.8480 (tmmt) cc_final: 0.7950 (tttm) REVERT: A 630 LYS cc_start: 0.7707 (mttp) cc_final: 0.7263 (mtmm) REVERT: A 637 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 643 MET cc_start: 0.8627 (tpp) cc_final: 0.8337 (mmm) REVERT: A 659 GLU cc_start: 0.7001 (pp20) cc_final: 0.6414 (tm-30) REVERT: A 663 MET cc_start: 0.8025 (ttm) cc_final: 0.7815 (ttm) REVERT: A 666 ASN cc_start: 0.7185 (t0) cc_final: 0.6823 (t0) REVERT: A 771 PHE cc_start: 0.8356 (m-80) cc_final: 0.8005 (m-80) REVERT: A 800 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 868 MET cc_start: 0.5537 (mtm) cc_final: 0.5030 (mtm) REVERT: C 14 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8394 (mtmt) REVERT: C 42 THR cc_start: 0.8565 (m) cc_final: 0.8211 (p) REVERT: C 44 GLU cc_start: 0.8065 (tt0) cc_final: 0.7824 (tt0) REVERT: C 95 PHE cc_start: 0.8202 (m-80) cc_final: 0.7724 (m-80) REVERT: C 176 PHE cc_start: 0.8261 (p90) cc_final: 0.7919 (p90) REVERT: C 269 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7908 (mtmm) REVERT: C 290 PHE cc_start: 0.8335 (m-80) cc_final: 0.8076 (m-80) outliers start: 38 outliers final: 19 residues processed: 258 average time/residue: 1.1666 time to fit residues: 324.5764 Evaluate side-chains 260 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 50.0000 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10283 Z= 0.220 Angle : 0.647 16.319 13920 Z= 0.319 Chirality : 0.044 0.199 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.231 23.075 1338 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.39 % Allowed : 19.73 % Favored : 77.88 % 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: 1.56 (0.25), residues: 1237 helix: 1.88 (0.21), residues: 624 sheet: 0.36 (0.38), residues: 199 loop : 0.21 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 810 HIS 0.005 0.001 HIS B 90 PHE 0.035 0.002 PHE A 640 TYR 0.036 0.002 TYR B 73 ARG 0.009 0.001 ARG A 121 *********************** 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 271 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7798 (t) cc_final: 0.7484 (t) REVERT: A 352 GLU cc_start: 0.6521 (tm-30) cc_final: 0.6188 (tm-30) REVERT: A 366 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7553 (tppt) REVERT: A 416 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 419 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7596 (ttmt) REVERT: A 488 GLU cc_start: 0.7863 (tp30) cc_final: 0.7540 (mm-30) REVERT: A 551 LYS cc_start: 0.7586 (mttm) cc_final: 0.7309 (mttm) REVERT: A 567 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7651 (mp0) REVERT: A 584 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6369 (tm-30) REVERT: A 590 MET cc_start: 0.8060 (mmm) cc_final: 0.7752 (tpt) REVERT: A 630 LYS cc_start: 0.7700 (mttp) cc_final: 0.7248 (mtmm) REVERT: A 637 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 643 MET cc_start: 0.8550 (tpp) cc_final: 0.8310 (mmm) REVERT: A 654 LEU cc_start: 0.8760 (tp) cc_final: 0.8553 (tt) REVERT: A 659 GLU cc_start: 0.7094 (pp20) cc_final: 0.6554 (tm-30) REVERT: A 666 ASN cc_start: 0.7192 (t0) cc_final: 0.6828 (t0) REVERT: A 771 PHE cc_start: 0.8330 (m-80) cc_final: 0.7997 (m-80) REVERT: A 868 MET cc_start: 0.5541 (mtm) cc_final: 0.5032 (mtm) REVERT: C 42 THR cc_start: 0.8566 (m) cc_final: 0.8290 (p) REVERT: C 44 GLU cc_start: 0.8061 (tt0) cc_final: 0.7821 (tt0) REVERT: C 95 PHE cc_start: 0.8129 (m-80) cc_final: 0.7757 (m-80) REVERT: C 176 PHE cc_start: 0.8255 (p90) cc_final: 0.7956 (p90) REVERT: C 269 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7894 (mtmm) REVERT: C 290 PHE cc_start: 0.8319 (m-80) cc_final: 0.8059 (m-80) outliers start: 27 outliers final: 21 residues processed: 256 average time/residue: 1.1838 time to fit residues: 326.6999 Evaluate side-chains 260 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 67 optimal weight: 0.0270 chunk 48 optimal weight: 0.0980 chunk 88 optimal weight: 0.0270 chunk 34 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS A 792 HIS C 115 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10283 Z= 0.188 Angle : 0.654 14.193 13920 Z= 0.321 Chirality : 0.044 0.173 1603 Planarity : 0.005 0.053 1761 Dihedral : 4.163 19.228 1338 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.30 % Allowed : 20.71 % Favored : 76.99 % 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: 1.49 (0.25), residues: 1237 helix: 1.80 (0.21), residues: 629 sheet: 0.44 (0.39), residues: 194 loop : 0.12 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 810 HIS 0.005 0.001 HIS B 90 PHE 0.027 0.002 PHE A 640 TYR 0.023 0.001 TYR B 73 ARG 0.008 0.000 ARG A 121 *********************** 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 273 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 SER cc_start: 0.7693 (t) cc_final: 0.7317 (p) REVERT: A 352 GLU cc_start: 0.6462 (tm-30) cc_final: 0.6147 (tm-30) REVERT: A 366 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7487 (tppt) REVERT: A 416 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6928 (mm-30) REVERT: A 419 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7565 (ttmt) REVERT: A 488 GLU cc_start: 0.7801 (tp30) cc_final: 0.7467 (mm-30) REVERT: A 551 LYS cc_start: 0.7597 (mttm) cc_final: 0.7310 (mttm) REVERT: A 567 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 584 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6323 (tm-30) REVERT: A 630 LYS cc_start: 0.7660 (mttp) cc_final: 0.7267 (mtmm) REVERT: A 632 MET cc_start: 0.7610 (ttm) cc_final: 0.7406 (ttp) REVERT: A 643 MET cc_start: 0.8535 (tpp) cc_final: 0.8279 (mmm) REVERT: A 654 LEU cc_start: 0.8723 (tp) cc_final: 0.8497 (tt) REVERT: A 659 GLU cc_start: 0.7114 (pp20) cc_final: 0.6652 (tm-30) REVERT: A 666 ASN cc_start: 0.7008 (t0) cc_final: 0.6655 (t0) REVERT: A 771 PHE cc_start: 0.8208 (m-80) cc_final: 0.7921 (m-80) REVERT: A 868 MET cc_start: 0.5542 (mtm) cc_final: 0.5031 (mtm) REVERT: C 42 THR cc_start: 0.8514 (m) cc_final: 0.8179 (p) REVERT: C 44 GLU cc_start: 0.8074 (tt0) cc_final: 0.7824 (tt0) REVERT: C 95 PHE cc_start: 0.8060 (m-80) cc_final: 0.7537 (m-80) REVERT: C 176 PHE cc_start: 0.8228 (p90) cc_final: 0.7878 (p90) REVERT: C 269 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7898 (mtmm) REVERT: C 290 PHE cc_start: 0.8296 (m-80) cc_final: 0.8027 (m-80) outliers start: 26 outliers final: 18 residues processed: 257 average time/residue: 1.1666 time to fit residues: 324.6422 Evaluate side-chains 256 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 chunk 124 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 40.0000 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS A 727 HIS C 115 ASN C 186 ASN C 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10283 Z= 0.276 Angle : 0.702 14.063 13920 Z= 0.348 Chirality : 0.046 0.251 1603 Planarity : 0.005 0.048 1761 Dihedral : 4.240 17.883 1338 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % Favored : 76.46 % 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: 1.43 (0.25), residues: 1237 helix: 1.71 (0.21), residues: 625 sheet: 0.39 (0.38), residues: 199 loop : 0.20 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 199 HIS 0.006 0.001 HIS A 596 PHE 0.028 0.002 PHE A 745 TYR 0.028 0.002 TYR B 73 ARG 0.008 0.001 ARG A 121 ********************** 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 253 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 201 SER cc_start: 0.7823 (t) cc_final: 0.7501 (t) REVERT: A 248 ARG cc_start: 0.6876 (tpt90) cc_final: 0.6599 (tpt90) REVERT: A 352 GLU cc_start: 0.6564 (tm-30) cc_final: 0.6227 (tm-30) REVERT: A 416 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 419 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7545 (ttmp) REVERT: A 488 GLU cc_start: 0.7886 (tp30) cc_final: 0.7553 (mm-30) REVERT: A 551 LYS cc_start: 0.7600 (mttm) cc_final: 0.7326 (mttm) REVERT: A 567 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7617 (mp0) REVERT: A 584 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6379 (tm-30) REVERT: A 595 LYS cc_start: 0.8466 (tmmt) cc_final: 0.7998 (tttm) REVERT: A 630 LYS cc_start: 0.7711 (mttp) cc_final: 0.7361 (mtmm) REVERT: A 643 MET cc_start: 0.8626 (tpp) cc_final: 0.8280 (mmm) REVERT: A 659 GLU cc_start: 0.7155 (pp20) cc_final: 0.6721 (tm-30) REVERT: A 661 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7389 (ttt-90) REVERT: A 666 ASN cc_start: 0.7143 (t0) cc_final: 0.6745 (t0) REVERT: A 771 PHE cc_start: 0.8266 (m-80) cc_final: 0.7991 (m-80) REVERT: A 868 MET cc_start: 0.5572 (mtm) cc_final: 0.5060 (mtm) REVERT: C 44 GLU cc_start: 0.8107 (tt0) cc_final: 0.7846 (tt0) REVERT: C 95 PHE cc_start: 0.8094 (m-80) cc_final: 0.7654 (m-80) REVERT: C 176 PHE cc_start: 0.8278 (p90) cc_final: 0.7892 (p90) REVERT: C 202 SER cc_start: 0.8660 (t) cc_final: 0.8444 (p) REVERT: C 269 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7952 (mtmm) REVERT: C 290 PHE cc_start: 0.8320 (m-80) cc_final: 0.8078 (m-80) outliers start: 20 outliers final: 16 residues processed: 240 average time/residue: 1.1961 time to fit residues: 309.4015 Evaluate side-chains 249 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 289 ASN 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: 0.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 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 727 HIS A 778 ASN C 115 ASN C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147025 restraints weight = 15690.295| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.46 r_work: 0.3713 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10283 Z= 0.319 Angle : 0.718 14.216 13920 Z= 0.354 Chirality : 0.046 0.179 1603 Planarity : 0.005 0.049 1761 Dihedral : 4.323 17.715 1338 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.50 % Allowed : 22.04 % Favored : 76.46 % 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: 1.61 (0.21), residues: 625 sheet: 0.36 (0.38), residues: 199 loop : 0.21 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 199 HIS 0.006 0.001 HIS A 596 PHE 0.027 0.002 PHE A 640 TYR 0.021 0.002 TYR B 73 ARG 0.009 0.001 ARG A 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.13 seconds wall clock time: 89 minutes 7.63 seconds (5347.63 seconds total)