Starting phenix.real_space_refine on Sat Jun 21 17:14:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.map" model { file = "/net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g40_51020/06_2025/9g40_51020.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 7932 2.51 5 N 2160 2.21 5 O 2285 1.98 5 H 12457 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24900 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 10098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 10098 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 15, 'TRANS': 601} Chain breaks: 2 Chain: "G" Number of atoms: 12901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 12901 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 26, 'TRANS': 770} Chain breaks: 3 Chain: "X" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 679 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 1 Chain: "u" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 611 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "v" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 611 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 11.73, per 1000 atoms: 0.47 Number of scatterers: 24900 At special positions: 0 Unit cell: (165.36, 127.2, 110.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 2285 8.00 N 2160 7.00 C 7932 6.00 H 12457 1.00 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: 6.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2942 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 76.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'F' and resid 249 through 262 removed outlier: 3.524A pdb=" N LEU F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.843A pdb=" N ASN F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 316 removed outlier: 3.788A pdb=" N GLU F 299 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU F 300 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY F 301 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 350 removed outlier: 3.508A pdb=" N GLN F 350 " --> pdb=" O HIS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 389 removed outlier: 5.675A pdb=" N ASP F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Proline residue: F 377 - end of helix Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.890A pdb=" N ALA F 400 " --> pdb=" O GLY F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 439 removed outlier: 3.631A pdb=" N HIS F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) Proline residue: F 428 - end of helix Processing helix chain 'F' and resid 461 through 466 removed outlier: 3.586A pdb=" N LYS F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 479 through 499 removed outlier: 3.997A pdb=" N HIS F 497 " --> pdb=" O ILE F 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 499 " --> pdb=" O PHE F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 556 Processing helix chain 'F' and resid 557 through 569 Processing helix chain 'F' and resid 573 through 589 removed outlier: 4.076A pdb=" N ILE F 577 " --> pdb=" O GLN F 573 " (cutoff:3.500A) Proline residue: F 586 - end of helix removed outlier: 3.926A pdb=" N VAL F 589 " --> pdb=" O LYS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.614A pdb=" N THR F 594 " --> pdb=" O PRO F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 611 removed outlier: 3.702A pdb=" N LEU F 600 " --> pdb=" O TYR F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 623 removed outlier: 3.545A pdb=" N ARG F 623 " --> pdb=" O GLU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 640 removed outlier: 4.168A pdb=" N VAL F 640 " --> pdb=" O THR F 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 640' Processing helix chain 'F' and resid 648 through 655 Processing helix chain 'F' and resid 656 through 694 removed outlier: 3.772A pdb=" N ARG F 692 " --> pdb=" O MET F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 729 Processing helix chain 'F' and resid 731 through 744 removed outlier: 3.771A pdb=" N ARG F 743 " --> pdb=" O ASN F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 765 Processing helix chain 'F' and resid 771 through 819 Processing helix chain 'F' and resid 825 through 869 Proline residue: F 844 - end of helix Processing helix chain 'F' and resid 874 through 883 Processing helix chain 'F' and resid 893 through 897 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 25 through 34 removed outlier: 3.741A pdb=" N LYS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 removed outlier: 3.674A pdb=" N PHE G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 74 removed outlier: 3.524A pdb=" N PHE G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 89 removed outlier: 3.962A pdb=" N MET G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 116 Processing helix chain 'G' and resid 149 through 170 removed outlier: 3.579A pdb=" N SER G 153 " --> pdb=" O THR G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'G' and resid 209 through 225 Processing helix chain 'G' and resid 253 through 264 Processing helix chain 'G' and resid 264 through 280 Processing helix chain 'G' and resid 281 through 284 removed outlier: 6.202A pdb=" N GLU G 284 " --> pdb=" O SER G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 281 through 284' Processing helix chain 'G' and resid 285 through 316 removed outlier: 4.275A pdb=" N ASN G 289 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN G 316 " --> pdb=" O GLN G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 349 removed outlier: 3.636A pdb=" N GLN G 329 " --> pdb=" O TRP G 325 " (cutoff:3.500A) Proline residue: G 330 - end of helix Processing helix chain 'G' and resid 352 through 366 Processing helix chain 'G' and resid 369 through 396 Proline residue: G 386 - end of helix Processing helix chain 'G' and resid 415 through 422 removed outlier: 4.323A pdb=" N ILE G 419 " --> pdb=" O ARG G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 445 removed outlier: 3.881A pdb=" N GLN G 444 " --> pdb=" O SER G 441 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS G 445 " --> pdb=" O PHE G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 463 removed outlier: 3.501A pdb=" N CYS G 463 " --> pdb=" O VAL G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 481 through 505 Processing helix chain 'G' and resid 508 through 519 Processing helix chain 'G' and resid 524 through 540 removed outlier: 5.466A pdb=" N GLU G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU G 538 " --> pdb=" O LEU G 534 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS G 540 " --> pdb=" O GLU G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 546 Processing helix chain 'G' and resid 547 through 561 removed outlier: 3.994A pdb=" N LEU G 551 " --> pdb=" O THR G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 591 Processing helix chain 'G' and resid 604 through 608 Processing helix chain 'G' and resid 631 through 662 removed outlier: 3.628A pdb=" N ASN G 662 " --> pdb=" O VAL G 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 663 through 667 removed outlier: 4.109A pdb=" N ARG G 667 " --> pdb=" O ALA G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 677 Processing helix chain 'G' and resid 678 through 699 removed outlier: 4.142A pdb=" N LEU G 682 " --> pdb=" O GLY G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 715 removed outlier: 3.768A pdb=" N ARG G 714 " --> pdb=" O GLU G 710 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 737 removed outlier: 3.537A pdb=" N VAL G 722 " --> pdb=" O ASN G 718 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS G 737 " --> pdb=" O CYS G 733 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 772 Processing helix chain 'G' and resid 823 through 851 removed outlier: 3.631A pdb=" N ALA G 834 " --> pdb=" O LYS G 830 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER G 849 " --> pdb=" O ILE G 845 " (cutoff:3.500A) Processing helix chain 'G' and resid 853 through 863 Processing helix chain 'G' and resid 865 through 868 removed outlier: 4.199A pdb=" N TYR G 868 " --> pdb=" O ASN G 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 865 through 868' Processing helix chain 'G' and resid 869 through 878 removed outlier: 3.611A pdb=" N GLU G 873 " --> pdb=" O THR G 869 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 878 " --> pdb=" O ARG G 874 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 46 removed outlier: 3.518A pdb=" N GLY X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 63 removed outlier: 4.206A pdb=" N LEU X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 80 Processing helix chain 'u' and resid 63 through 91 removed outlier: 4.406A pdb=" N LEU u 77 " --> pdb=" O GLU u 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS u 78 " --> pdb=" O ASN u 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR u 82 " --> pdb=" O LYS u 78 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU u 91 " --> pdb=" O ARG u 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 59 through 91 removed outlier: 3.680A pdb=" N PHE v 63 " --> pdb=" O ASN v 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU v 64 " --> pdb=" O MET v 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU v 91 " --> pdb=" O ARG v 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 270 through 272 removed outlier: 3.527A pdb=" N CYS F 277 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 624 through 628 removed outlier: 3.760A pdb=" N ASP F 644 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 233 through 236 removed outlier: 3.844A pdb=" N THR G 245 " --> pdb=" O GLN G 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 409 through 411 Processing sheet with id=AA5, first strand: chain 'G' and resid 573 through 577 841 hydrogen bonds defined for protein. 2472 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: 8.66 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12434 1.03 - 1.23: 23 1.23 - 1.42: 5347 1.42 - 1.62: 7233 1.62 - 1.81: 109 Bond restraints: 25146 Sorted by residual: bond pdb=" CA ARG G 184 " pdb=" CB ARG G 184 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.97e+00 bond pdb=" CA ARG G 184 " pdb=" C ARG G 184 " ideal model delta sigma weight residual 1.531 1.523 0.008 7.40e-03 1.83e+04 1.29e+00 bond pdb=" CB PRO G 440 " pdb=" CG PRO G 440 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.09e+00 bond pdb=" CA ALA G 673 " pdb=" CB ALA G 673 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.38e-01 bond pdb=" CA GLU G 284 " pdb=" C GLU G 284 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 7.02e-01 ... (remaining 25141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 43261 1.16 - 2.31: 2027 2.31 - 3.47: 70 3.47 - 4.63: 27 4.63 - 5.78: 5 Bond angle restraints: 45390 Sorted by residual: angle pdb=" N ALA G 673 " pdb=" CA ALA G 673 " pdb=" CB ALA G 673 " ideal model delta sigma weight residual 114.17 110.06 4.11 1.14e+00 7.69e-01 1.30e+01 angle pdb=" CA GLU G 284 " pdb=" C GLU G 284 " pdb=" N TYR G 285 " ideal model delta sigma weight residual 116.84 122.62 -5.78 1.71e+00 3.42e-01 1.14e+01 angle pdb=" CA GLU G 284 " pdb=" C GLU G 284 " pdb=" O GLU G 284 " ideal model delta sigma weight residual 120.51 116.59 3.92 1.43e+00 4.89e-01 7.50e+00 angle pdb=" N ASN G 77 " pdb=" CA ASN G 77 " pdb=" CB ASN G 77 " ideal model delta sigma weight residual 113.65 110.02 3.63 1.47e+00 4.63e-01 6.09e+00 angle pdb=" N LEU G 264 " pdb=" CA LEU G 264 " pdb=" C LEU G 264 " ideal model delta sigma weight residual 109.81 115.25 -5.44 2.21e+00 2.05e-01 6.06e+00 ... (remaining 45385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 10879 16.96 - 33.92: 634 33.92 - 50.89: 162 50.89 - 67.85: 60 67.85 - 84.81: 7 Dihedral angle restraints: 11742 sinusoidal: 6377 harmonic: 5365 Sorted by residual: dihedral pdb=" CA ASP G 253 " pdb=" CB ASP G 253 " pdb=" CG ASP G 253 " pdb=" OD1 ASP G 253 " ideal model delta sinusoidal sigma weight residual -30.00 -87.93 57.93 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" N ASP G 220 " pdb=" CA ASP G 220 " pdb=" CB ASP G 220 " pdb=" CG ASP G 220 " ideal model delta sinusoidal sigma weight residual -180.00 -120.06 -59.94 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASN G 831 " pdb=" CA ASN G 831 " pdb=" CB ASN G 831 " pdb=" CG ASN G 831 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1344 0.028 - 0.056: 427 0.056 - 0.084: 87 0.084 - 0.112: 45 0.112 - 0.140: 11 Chirality restraints: 1914 Sorted by residual: chirality pdb=" CA ILE F 474 " pdb=" N ILE F 474 " pdb=" C ILE F 474 " pdb=" CB ILE F 474 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL F 626 " pdb=" N VAL F 626 " pdb=" C VAL F 626 " pdb=" CB VAL F 626 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL F 280 " pdb=" N VAL F 280 " pdb=" C VAL F 280 " pdb=" CB VAL F 280 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1911 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 376 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 377 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 377 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 377 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 688 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASN G 688 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN G 688 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE G 689 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 685 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG G 685 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG G 685 " 0.009 2.00e-02 2.50e+03 pdb=" N MET G 686 " 0.008 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1154 2.15 - 2.77: 49287 2.77 - 3.38: 71626 3.38 - 3.99: 83656 3.99 - 4.60: 132179 Nonbonded interactions: 337902 Sorted by model distance: nonbonded pdb=" OE1 GLU G 538 " pdb=" H GLU G 538 " model vdw 1.543 2.450 nonbonded pdb=" OE1 GLU G 537 " pdb=" H GLU G 537 " model vdw 1.568 2.450 nonbonded pdb=" OE1 GLU G 93 " pdb=" H GLU G 93 " model vdw 1.571 2.450 nonbonded pdb=" OE1 GLU G 536 " pdb=" H GLU G 536 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU G 413 " pdb=" H GLU G 413 " model vdw 1.591 2.450 ... (remaining 337897 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 Found NCS groups: ncs_group { reference = chain 'u' selection = chain 'v' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.430 Extract box with map and model: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.002 0.052 12689 Z= 0.109 Angle : 0.469 5.784 17124 Z= 0.267 Chirality : 0.032 0.140 1914 Planarity : 0.003 0.045 2182 Dihedral : 11.676 84.808 4757 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.28 % Allowed : 7.42 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1505 helix: 2.21 (0.16), residues: 1054 sheet: -1.27 (1.57), residues: 10 loop : -1.12 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 638 HIS 0.003 0.001 HIS G 580 PHE 0.010 0.001 PHE F 327 TYR 0.010 0.001 TYR G 484 ARG 0.003 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.12818 ( 841) hydrogen bonds : angle 5.35870 ( 2472) covalent geometry : bond 0.00210 (12689) covalent geometry : angle 0.46867 (17124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 292 ASP cc_start: 0.7881 (m-30) cc_final: 0.7674 (m-30) REVERT: F 299 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8257 (pm20) REVERT: F 336 ARG cc_start: 0.8841 (tmm160) cc_final: 0.8543 (ttp80) REVERT: F 371 LEU cc_start: 0.9386 (mp) cc_final: 0.9186 (mm) REVERT: F 379 MET cc_start: 0.8882 (mtt) cc_final: 0.8649 (tmm) REVERT: F 605 GLU cc_start: 0.9097 (tp30) cc_final: 0.8894 (tp30) REVERT: F 708 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5911 (m90) REVERT: F 723 TYR cc_start: 0.8553 (t80) cc_final: 0.7476 (t80) REVERT: F 797 ARG cc_start: 0.9116 (tpt-90) cc_final: 0.8735 (tpp-160) REVERT: G 39 TYR cc_start: 0.8503 (p90) cc_final: 0.8068 (p90) REVERT: G 221 LEU cc_start: 0.9496 (mt) cc_final: 0.9260 (mt) REVERT: G 238 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6305 (mp) REVERT: G 698 MET cc_start: 0.7367 (ttp) cc_final: 0.6891 (mmm) REVERT: G 715 SER cc_start: 0.9669 (m) cc_final: 0.9355 (p) REVERT: G 864 PHE cc_start: 0.8862 (t80) cc_final: 0.8342 (p90) REVERT: X 57 LEU cc_start: 0.9143 (mm) cc_final: 0.8900 (tp) REVERT: v 60 MET cc_start: 0.7994 (ptt) cc_final: 0.7667 (tmm) outliers start: 31 outliers final: 13 residues processed: 225 average time/residue: 0.5775 time to fit residues: 183.7407 Evaluate side-chains 166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.068135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.055794 restraints weight = 216137.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057922 restraints weight = 111152.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.059423 restraints weight = 69887.908| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12689 Z= 0.155 Angle : 0.559 6.703 17124 Z= 0.310 Chirality : 0.035 0.137 1914 Planarity : 0.005 0.077 2182 Dihedral : 3.743 17.336 1675 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1505 helix: 2.03 (0.16), residues: 1056 sheet: -1.10 (1.50), residues: 10 loop : -1.36 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 638 HIS 0.010 0.001 HIS G 580 PHE 0.021 0.002 PHE G 832 TYR 0.014 0.001 TYR G 327 ARG 0.006 0.000 ARG F 675 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 841) hydrogen bonds : angle 4.63834 ( 2472) covalent geometry : bond 0.00327 (12689) covalent geometry : angle 0.55898 (17124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 292 ASP cc_start: 0.7683 (m-30) cc_final: 0.7479 (m-30) REVERT: F 299 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8256 (mt-10) REVERT: F 336 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8487 (ttp80) REVERT: F 371 LEU cc_start: 0.9502 (mp) cc_final: 0.9282 (mm) REVERT: F 496 LEU cc_start: 0.9551 (mt) cc_final: 0.9344 (mt) REVERT: F 605 GLU cc_start: 0.9028 (tp30) cc_final: 0.8797 (tp30) REVERT: F 797 ARG cc_start: 0.9147 (tpt-90) cc_final: 0.8778 (tpp-160) REVERT: G 39 TYR cc_start: 0.8171 (p90) cc_final: 0.7813 (p90) REVERT: G 221 LEU cc_start: 0.9380 (mt) cc_final: 0.9103 (mt) REVERT: G 258 GLU cc_start: 0.8863 (tt0) cc_final: 0.8445 (tp30) REVERT: G 446 MET cc_start: 0.8298 (mmm) cc_final: 0.8075 (mmm) REVERT: G 698 MET cc_start: 0.7964 (ttp) cc_final: 0.7737 (mmm) REVERT: v 60 MET cc_start: 0.8070 (ptt) cc_final: 0.7677 (tmm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.6036 time to fit residues: 151.6103 Evaluate side-chains 154 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 597 GLN ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.066654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054359 restraints weight = 220595.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.056438 restraints weight = 113941.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057858 restraints weight = 71881.791| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12689 Z= 0.236 Angle : 0.567 5.690 17124 Z= 0.328 Chirality : 0.035 0.142 1914 Planarity : 0.005 0.053 2182 Dihedral : 3.898 16.266 1675 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1505 helix: 1.72 (0.16), residues: 1058 sheet: -3.67 (1.06), residues: 12 loop : -1.77 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 638 HIS 0.008 0.001 HIS G 580 PHE 0.017 0.002 PHE G 326 TYR 0.028 0.002 TYR G 427 ARG 0.010 0.000 ARG G 415 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 841) hydrogen bonds : angle 4.73747 ( 2472) covalent geometry : bond 0.00466 (12689) covalent geometry : angle 0.56700 (17124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 299 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 496 LEU cc_start: 0.9582 (mt) cc_final: 0.9299 (mt) REVERT: F 797 ARG cc_start: 0.9154 (tpt-90) cc_final: 0.8792 (tpp-160) REVERT: G 39 TYR cc_start: 0.8256 (p90) cc_final: 0.7888 (p90) REVERT: G 561 MET cc_start: 0.8102 (tmm) cc_final: 0.7699 (tmm) REVERT: u 65 ASN cc_start: 0.9342 (p0) cc_final: 0.8717 (p0) REVERT: v 60 MET cc_start: 0.8044 (ptt) cc_final: 0.7675 (tmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.5966 time to fit residues: 142.8702 Evaluate side-chains 145 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 35 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.067649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055171 restraints weight = 216474.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057391 restraints weight = 109241.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058913 restraints weight = 67211.784| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12689 Z= 0.126 Angle : 0.511 5.249 17124 Z= 0.282 Chirality : 0.034 0.134 1914 Planarity : 0.004 0.066 2182 Dihedral : 3.827 17.219 1675 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1505 helix: 1.89 (0.16), residues: 1064 sheet: -3.38 (1.16), residues: 12 loop : -1.50 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 463 HIS 0.006 0.001 HIS G 580 PHE 0.026 0.001 PHE G 828 TYR 0.012 0.001 TYR G 484 ARG 0.003 0.000 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 841) hydrogen bonds : angle 4.38414 ( 2472) covalent geometry : bond 0.00272 (12689) covalent geometry : angle 0.51093 (17124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 299 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8246 (mt-10) REVERT: F 723 TYR cc_start: 0.7994 (t80) cc_final: 0.7192 (t80) REVERT: F 797 ARG cc_start: 0.9123 (tpt-90) cc_final: 0.8765 (tpp-160) REVERT: G 39 TYR cc_start: 0.8163 (p90) cc_final: 0.7957 (p90) REVERT: G 408 MET cc_start: 0.8185 (mmp) cc_final: 0.7863 (mmp) REVERT: v 60 MET cc_start: 0.8064 (ptt) cc_final: 0.7664 (tmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5578 time to fit residues: 135.5874 Evaluate side-chains 143 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 140 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.067316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054835 restraints weight = 218683.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.056999 restraints weight = 110520.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058493 restraints weight = 68461.536| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12689 Z= 0.162 Angle : 0.510 5.649 17124 Z= 0.287 Chirality : 0.034 0.130 1914 Planarity : 0.004 0.046 2182 Dihedral : 3.802 15.909 1675 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1505 helix: 1.88 (0.16), residues: 1064 sheet: -3.41 (1.12), residues: 12 loop : -1.56 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 638 HIS 0.006 0.001 HIS F 754 PHE 0.013 0.001 PHE G 326 TYR 0.017 0.001 TYR G 427 ARG 0.004 0.000 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 841) hydrogen bonds : angle 4.40070 ( 2472) covalent geometry : bond 0.00335 (12689) covalent geometry : angle 0.50992 (17124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 299 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8283 (mt-10) REVERT: F 723 TYR cc_start: 0.8009 (t80) cc_final: 0.7208 (t80) REVERT: F 797 ARG cc_start: 0.9133 (tpt-90) cc_final: 0.8792 (tpp-160) REVERT: G 39 TYR cc_start: 0.8076 (p90) cc_final: 0.7844 (p90) REVERT: u 65 ASN cc_start: 0.9503 (p0) cc_final: 0.9011 (p0) REVERT: v 60 MET cc_start: 0.8201 (ptt) cc_final: 0.7764 (tmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.5484 time to fit residues: 128.2899 Evaluate side-chains 141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.067776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055249 restraints weight = 215617.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057488 restraints weight = 108751.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058990 restraints weight = 66994.260| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12689 Z= 0.131 Angle : 0.505 5.868 17124 Z= 0.280 Chirality : 0.034 0.132 1914 Planarity : 0.004 0.049 2182 Dihedral : 3.772 17.462 1675 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1505 helix: 1.88 (0.16), residues: 1070 sheet: -1.28 (1.43), residues: 10 loop : -1.52 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 638 HIS 0.005 0.001 HIS G 580 PHE 0.031 0.001 PHE G 828 TYR 0.028 0.001 TYR G 427 ARG 0.003 0.000 ARG F 318 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 841) hydrogen bonds : angle 4.29887 ( 2472) covalent geometry : bond 0.00281 (12689) covalent geometry : angle 0.50515 (17124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 292 ASP cc_start: 0.8008 (m-30) cc_final: 0.7807 (m-30) REVERT: F 299 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8261 (mt-10) REVERT: F 481 ASP cc_start: 0.9467 (m-30) cc_final: 0.9086 (p0) REVERT: F 723 TYR cc_start: 0.8030 (t80) cc_final: 0.7259 (t80) REVERT: F 797 ARG cc_start: 0.9124 (tpt-90) cc_final: 0.8786 (tpp-160) REVERT: G 39 TYR cc_start: 0.8184 (p90) cc_final: 0.7972 (p90) REVERT: G 408 MET cc_start: 0.8192 (mmp) cc_final: 0.7900 (mmp) REVERT: v 60 MET cc_start: 0.8204 (ptt) cc_final: 0.7760 (tmm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.5581 time to fit residues: 133.8219 Evaluate side-chains 144 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.067505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055052 restraints weight = 216010.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.057223 restraints weight = 109127.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.058707 restraints weight = 67695.469| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12689 Z= 0.140 Angle : 0.505 6.674 17124 Z= 0.278 Chirality : 0.034 0.167 1914 Planarity : 0.004 0.047 2182 Dihedral : 3.752 16.069 1675 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1505 helix: 1.90 (0.16), residues: 1071 sheet: -1.28 (1.34), residues: 10 loop : -1.55 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 624 HIS 0.005 0.001 HIS G 580 PHE 0.015 0.001 PHE F 432 TYR 0.029 0.001 TYR G 427 ARG 0.003 0.000 ARG F 318 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 841) hydrogen bonds : angle 4.26323 ( 2472) covalent geometry : bond 0.00294 (12689) covalent geometry : angle 0.50489 (17124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 292 ASP cc_start: 0.8071 (m-30) cc_final: 0.7860 (m-30) REVERT: F 299 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 481 ASP cc_start: 0.9503 (m-30) cc_final: 0.9097 (p0) REVERT: F 723 TYR cc_start: 0.8053 (t80) cc_final: 0.7271 (t80) REVERT: F 797 ARG cc_start: 0.9141 (tpt-90) cc_final: 0.8798 (tpp-160) REVERT: G 715 SER cc_start: 0.9481 (m) cc_final: 0.9077 (p) REVERT: u 65 ASN cc_start: 0.9514 (p0) cc_final: 0.8951 (p0) REVERT: v 60 MET cc_start: 0.8197 (ptt) cc_final: 0.7760 (tmm) REVERT: v 78 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8691 (mmmt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.5529 time to fit residues: 133.5340 Evaluate side-chains 148 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.067022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054652 restraints weight = 218795.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.056779 restraints weight = 112663.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058244 restraints weight = 70506.445| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12689 Z= 0.196 Angle : 0.534 5.917 17124 Z= 0.302 Chirality : 0.034 0.159 1914 Planarity : 0.004 0.045 2182 Dihedral : 3.826 16.072 1675 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1505 helix: 1.72 (0.16), residues: 1076 sheet: -3.31 (1.08), residues: 12 loop : -1.76 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 624 HIS 0.008 0.001 HIS F 687 PHE 0.013 0.002 PHE F 432 TYR 0.020 0.001 TYR G 404 ARG 0.004 0.000 ARG F 764 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 841) hydrogen bonds : angle 4.43082 ( 2472) covalent geometry : bond 0.00394 (12689) covalent geometry : angle 0.53443 (17124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 292 ASP cc_start: 0.8130 (m-30) cc_final: 0.7928 (m-30) REVERT: F 299 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8291 (mt-10) REVERT: F 581 MET cc_start: 0.8765 (ttt) cc_final: 0.8518 (ttt) REVERT: F 797 ARG cc_start: 0.9116 (tpt-90) cc_final: 0.8802 (tpp-160) REVERT: G 39 TYR cc_start: 0.8200 (p90) cc_final: 0.7903 (p90) REVERT: G 408 MET cc_start: 0.8351 (mmp) cc_final: 0.7822 (mmp) REVERT: G 715 SER cc_start: 0.9544 (m) cc_final: 0.9199 (p) REVERT: u 65 ASN cc_start: 0.9530 (p0) cc_final: 0.9002 (p0) REVERT: v 60 MET cc_start: 0.8184 (ptt) cc_final: 0.7868 (tmm) REVERT: v 78 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8691 (mmmt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.5900 time to fit residues: 144.9936 Evaluate side-chains 145 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.067167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054600 restraints weight = 218511.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.056803 restraints weight = 110080.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058299 restraints weight = 68074.954| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12689 Z= 0.150 Angle : 0.518 5.872 17124 Z= 0.287 Chirality : 0.034 0.147 1914 Planarity : 0.004 0.097 2182 Dihedral : 3.832 16.161 1675 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1505 helix: 1.76 (0.16), residues: 1076 sheet: -1.38 (1.24), residues: 10 loop : -1.72 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 624 HIS 0.005 0.001 HIS F 687 PHE 0.021 0.001 PHE F 839 TYR 0.019 0.001 TYR G 404 ARG 0.003 0.000 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 841) hydrogen bonds : angle 4.30126 ( 2472) covalent geometry : bond 0.00316 (12689) covalent geometry : angle 0.51770 (17124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 250 GLU cc_start: 0.7992 (tp30) cc_final: 0.7593 (tp30) REVERT: F 292 ASP cc_start: 0.8065 (m-30) cc_final: 0.7858 (m-30) REVERT: F 299 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8264 (mt-10) REVERT: F 481 ASP cc_start: 0.9430 (m-30) cc_final: 0.9014 (p0) REVERT: F 797 ARG cc_start: 0.9099 (tpt-90) cc_final: 0.8791 (tpp-160) REVERT: G 39 TYR cc_start: 0.8230 (p90) cc_final: 0.7927 (p90) REVERT: G 715 SER cc_start: 0.9547 (m) cc_final: 0.9205 (p) REVERT: u 65 ASN cc_start: 0.9503 (p0) cc_final: 0.8982 (p0) REVERT: v 60 MET cc_start: 0.8201 (ptt) cc_final: 0.7926 (tmm) REVERT: v 78 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8696 (mmmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.5566 time to fit residues: 133.5860 Evaluate side-chains 147 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055050 restraints weight = 213867.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.057305 restraints weight = 107015.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058793 restraints weight = 65590.130| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12689 Z= 0.118 Angle : 0.507 6.693 17124 Z= 0.276 Chirality : 0.034 0.143 1914 Planarity : 0.004 0.085 2182 Dihedral : 3.777 15.705 1675 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1505 helix: 1.91 (0.16), residues: 1070 sheet: -1.30 (1.29), residues: 10 loop : -1.54 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 638 HIS 0.004 0.001 HIS F 716 PHE 0.019 0.001 PHE F 432 TYR 0.017 0.001 TYR G 404 ARG 0.005 0.000 ARG G 871 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 841) hydrogen bonds : angle 4.15967 ( 2472) covalent geometry : bond 0.00264 (12689) covalent geometry : angle 0.50669 (17124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 250 GLU cc_start: 0.7819 (tp30) cc_final: 0.7536 (tp30) REVERT: F 292 ASP cc_start: 0.8060 (m-30) cc_final: 0.7850 (m-30) REVERT: F 299 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8231 (mt-10) REVERT: F 481 ASP cc_start: 0.9443 (m-30) cc_final: 0.9053 (p0) REVERT: F 723 TYR cc_start: 0.8011 (t80) cc_final: 0.7207 (t80) REVERT: F 797 ARG cc_start: 0.9100 (tpt-90) cc_final: 0.8785 (tpp-160) REVERT: G 39 TYR cc_start: 0.8124 (p90) cc_final: 0.7805 (p90) REVERT: G 258 GLU cc_start: 0.8930 (tt0) cc_final: 0.8249 (tp30) REVERT: G 446 MET cc_start: 0.8469 (mmm) cc_final: 0.8113 (mmm) REVERT: G 715 SER cc_start: 0.9519 (m) cc_final: 0.9176 (p) REVERT: G 752 MET cc_start: 0.8622 (mmm) cc_final: 0.8383 (mmm) REVERT: u 65 ASN cc_start: 0.9497 (p0) cc_final: 0.8943 (p0) REVERT: v 60 MET cc_start: 0.8199 (ptt) cc_final: 0.7876 (tmm) REVERT: v 78 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8615 (mmmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.5588 time to fit residues: 133.9509 Evaluate side-chains 149 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 37 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055080 restraints weight = 215526.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.057299 restraints weight = 108204.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.058802 restraints weight = 66699.073| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12689 Z= 0.120 Angle : 0.502 6.873 17124 Z= 0.274 Chirality : 0.033 0.130 1914 Planarity : 0.004 0.076 2182 Dihedral : 3.739 16.292 1675 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1505 helix: 1.94 (0.16), residues: 1073 sheet: -1.26 (1.32), residues: 10 loop : -1.58 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 624 HIS 0.004 0.001 HIS F 716 PHE 0.018 0.001 PHE F 432 TYR 0.016 0.001 TYR G 404 ARG 0.004 0.000 ARG G 871 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 841) hydrogen bonds : angle 4.12490 ( 2472) covalent geometry : bond 0.00260 (12689) covalent geometry : angle 0.50152 (17124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7334.56 seconds wall clock time: 126 minutes 39.25 seconds (7599.25 seconds total)