Starting phenix.real_space_refine on Fri Sep 19 10:03:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g40_51020/09_2025/9g40_51020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g40_51020/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9g40_51020/09_2025/9g40_51020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g40_51020/09_2025/9g40_51020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g40_51020/09_2025/9g40_51020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g40_51020/09_2025/9g40_51020.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.40, per 1000 atoms: 0.18 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: 2.28 Conformation dependent library (CDL) restraints added in 739.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.60 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: 5.27 Time building geometry restraints manager: 3.14 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: 2.030 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: 0.140 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.570 Find NCS groups from input model: 0.160 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- 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 : 11.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG G 76 TYR 0.010 0.001 TYR G 484 PHE 0.010 0.001 PHE F 327 TRP 0.008 0.001 TRP F 638 HIS 0.003 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00210 (12689) covalent geometry : angle 0.46867 (17124) hydrogen bonds : bond 0.12818 ( 841) hydrogen bonds : angle 5.35870 ( 2472) *********************** 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 : 0.579 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: 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: 0.8416 (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: 0.9261 (mt) REVERT: G 238 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6306 (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: 0.2776 time to fit residues: 87.9154 Evaluate side-chains 165 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0010 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.8992 ------------------------------------------------------------------------------- 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 458 ASN G 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055329 restraints weight = 217496.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.057539 restraints weight = 111769.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059003 restraints weight = 69380.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.059972 restraints weight = 49402.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.060606 restraints weight = 38782.357| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12689 Z= 0.188 Angle : 0.568 7.267 17124 Z= 0.320 Chirality : 0.035 0.134 1914 Planarity : 0.005 0.076 2182 Dihedral : 3.777 17.458 1675 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1505 helix: 1.93 (0.16), residues: 1061 sheet: -1.08 (1.56), residues: 10 loop : -1.46 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 890 TYR 0.018 0.001 TYR G 327 PHE 0.019 0.002 PHE F 839 TRP 0.014 0.001 TRP F 638 HIS 0.010 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00384 (12689) covalent geometry : angle 0.56786 (17124) hydrogen bonds : bond 0.04830 ( 841) hydrogen bonds : angle 4.75003 ( 2472) *********************** 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 176 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.721 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 292 ASP cc_start: 0.7667 (m-30) cc_final: 0.7460 (m-30) REVERT: F 299 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8244 (mt-10) REVERT: F 371 LEU cc_start: 0.9503 (mp) cc_final: 0.9281 (mm) REVERT: F 496 LEU cc_start: 0.9553 (mt) cc_final: 0.9343 (mt) REVERT: F 797 ARG cc_start: 0.9103 (tpt-90) cc_final: 0.8746 (tpp-160) REVERT: F 804 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 39 TYR cc_start: 0.8196 (p90) cc_final: 0.7835 (p90) REVERT: G 221 LEU cc_start: 0.9418 (mt) cc_final: 0.9157 (mt) REVERT: G 258 GLU cc_start: 0.8917 (tt0) cc_final: 0.8238 (tp30) REVERT: G 446 MET cc_start: 0.8374 (mmm) cc_final: 0.8151 (mmm) REVERT: G 698 MET cc_start: 0.7940 (ttp) cc_final: 0.7662 (mmm) REVERT: v 60 MET cc_start: 0.8073 (ptt) cc_final: 0.7701 (tmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2869 time to fit residues: 71.0303 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 : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 35 ASN G 329 GLN G 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053998 restraints weight = 220311.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.056063 restraints weight = 113923.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.057502 restraints weight = 71907.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058457 restraints weight = 51621.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.059072 restraints weight = 40842.045| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12689 Z= 0.255 Angle : 0.584 5.775 17124 Z= 0.338 Chirality : 0.035 0.155 1914 Planarity : 0.005 0.052 2182 Dihedral : 3.977 16.735 1675 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.22), residues: 1505 helix: 1.56 (0.16), residues: 1059 sheet: -3.70 (1.08), residues: 12 loop : -1.92 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 415 TYR 0.027 0.002 TYR G 427 PHE 0.018 0.002 PHE G 326 TRP 0.008 0.001 TRP F 638 HIS 0.008 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00498 (12689) covalent geometry : angle 0.58384 (17124) hydrogen bonds : bond 0.04628 ( 841) hydrogen bonds : angle 4.84443 ( 2472) *********************** 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 165 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.638 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: 0.8600 (mt-10) cc_final: 0.8137 (mt-10) REVERT: F 371 LEU cc_start: 0.9536 (mp) cc_final: 0.9314 (mm) REVERT: F 797 ARG cc_start: 0.9100 (tpt-90) cc_final: 0.8758 (tpp-160) REVERT: F 804 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8939 (tm-30) REVERT: F 835 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7722 (mtt90) REVERT: G 39 TYR cc_start: 0.8229 (p90) cc_final: 0.7850 (p90) REVERT: G 561 MET cc_start: 0.8132 (tmm) cc_final: 0.7688 (tmm) REVERT: G 769 MET cc_start: 0.8115 (tmm) cc_final: 0.7829 (tmm) REVERT: u 65 ASN cc_start: 0.9455 (p0) cc_final: 0.8737 (p0) REVERT: v 60 MET cc_start: 0.8054 (ptt) cc_final: 0.7710 (tmm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2596 time to fit residues: 61.4847 Evaluate side-chains 146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.067129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054695 restraints weight = 215311.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.056878 restraints weight = 108018.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058338 restraints weight = 66691.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.059321 restraints weight = 47394.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059974 restraints weight = 37087.412| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2621 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= 0.150 Angle : 0.530 5.989 17124 Z= 0.298 Chirality : 0.034 0.163 1914 Planarity : 0.004 0.077 2182 Dihedral : 3.923 17.273 1675 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1505 helix: 1.75 (0.16), residues: 1061 sheet: -3.60 (1.13), residues: 12 loop : -1.70 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 415 TYR 0.023 0.001 TYR G 427 PHE 0.024 0.002 PHE G 828 TRP 0.007 0.001 TRP F 463 HIS 0.007 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00316 (12689) covalent geometry : angle 0.53011 (17124) hydrogen bonds : bond 0.04334 ( 841) hydrogen bonds : angle 4.52020 ( 2472) *********************** 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 163 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.596 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: F 299 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 371 LEU cc_start: 0.9507 (mp) cc_final: 0.9307 (mm) REVERT: F 723 TYR cc_start: 0.8068 (t80) cc_final: 0.7283 (t80) REVERT: F 797 ARG cc_start: 0.9084 (tpt-90) cc_final: 0.8753 (tpp-160) REVERT: F 804 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8970 (tm-30) REVERT: F 835 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7702 (mtt90) REVERT: G 39 TYR cc_start: 0.8001 (p90) cc_final: 0.7483 (p90) REVERT: G 408 MET cc_start: 0.8275 (mmp) cc_final: 0.7926 (mmp) REVERT: G 769 MET cc_start: 0.8133 (tmm) cc_final: 0.7853 (tmm) REVERT: v 60 MET cc_start: 0.8052 (ptt) cc_final: 0.7694 (tmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2440 time to fit residues: 57.0215 Evaluate side-chains 137 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** G 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.067471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054817 restraints weight = 216595.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.057025 restraints weight = 109528.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.058536 restraints weight = 67908.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059523 restraints weight = 48216.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.060178 restraints weight = 37795.668| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12689 Z= 0.128 Angle : 0.510 6.472 17124 Z= 0.283 Chirality : 0.034 0.133 1914 Planarity : 0.004 0.049 2182 Dihedral : 3.830 16.016 1675 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.22), residues: 1505 helix: 1.86 (0.16), residues: 1061 sheet: -1.55 (1.39), residues: 10 loop : -1.57 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 415 TYR 0.010 0.001 TYR G 67 PHE 0.021 0.001 PHE G 832 TRP 0.006 0.001 TRP F 463 HIS 0.006 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00273 (12689) covalent geometry : angle 0.51000 (17124) hydrogen bonds : bond 0.04023 ( 841) hydrogen bonds : angle 4.35682 ( 2472) *********************** 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 161 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.691 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: F 299 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8221 (mt-10) REVERT: F 371 LEU cc_start: 0.9532 (mp) cc_final: 0.9297 (mm) REVERT: F 723 TYR cc_start: 0.8051 (t80) cc_final: 0.7276 (t80) REVERT: F 797 ARG cc_start: 0.9088 (tpt-90) cc_final: 0.8756 (tpp-160) REVERT: F 804 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8972 (tm-30) REVERT: G 39 TYR cc_start: 0.8035 (p90) cc_final: 0.7509 (p90) REVERT: G 769 MET cc_start: 0.8098 (tmm) cc_final: 0.7896 (tmm) REVERT: u 65 ASN cc_start: 0.9313 (p0) cc_final: 0.8653 (p0) REVERT: v 60 MET cc_start: 0.8182 (ptt) cc_final: 0.7776 (tmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2331 time to fit residues: 54.6470 Evaluate side-chains 142 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.0070 chunk 124 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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** G 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.067839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055269 restraints weight = 214459.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.057490 restraints weight = 108580.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059007 restraints weight = 67071.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059994 restraints weight = 47440.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060620 restraints weight = 37131.443| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12689 Z= 0.119 Angle : 0.502 5.967 17124 Z= 0.276 Chirality : 0.034 0.135 1914 Planarity : 0.004 0.049 2182 Dihedral : 3.770 17.421 1675 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.22), residues: 1505 helix: 1.93 (0.16), residues: 1061 sheet: -1.48 (1.46), residues: 10 loop : -1.47 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 318 TYR 0.022 0.001 TYR G 404 PHE 0.029 0.001 PHE G 828 TRP 0.006 0.001 TRP G 180 HIS 0.006 0.001 HIS F 754 Details of bonding type rmsd covalent geometry : bond 0.00256 (12689) covalent geometry : angle 0.50185 (17124) hydrogen bonds : bond 0.03955 ( 841) hydrogen bonds : angle 4.28179 ( 2472) *********************** 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 166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.580 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 299 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8204 (mt-10) REVERT: F 481 ASP cc_start: 0.9423 (m-30) cc_final: 0.9060 (p0) REVERT: F 723 TYR cc_start: 0.8023 (t80) cc_final: 0.7229 (t80) REVERT: F 797 ARG cc_start: 0.9084 (tpt-90) cc_final: 0.8753 (tpp-160) REVERT: F 804 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8987 (tm-30) REVERT: G 39 TYR cc_start: 0.8040 (p90) cc_final: 0.7513 (p90) REVERT: G 408 MET cc_start: 0.8270 (mmp) cc_final: 0.8065 (mmp) REVERT: G 769 MET cc_start: 0.8078 (tmm) cc_final: 0.7870 (tmm) REVERT: v 60 MET cc_start: 0.8180 (ptt) cc_final: 0.7786 (tmm) REVERT: v 78 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8739 (mmmt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2513 time to fit residues: 60.4064 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 : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 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 G 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055237 restraints weight = 215475.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057355 restraints weight = 110176.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058823 restraints weight = 68796.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059769 restraints weight = 49073.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060409 restraints weight = 38711.371| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2945 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= 0.127 Angle : 0.500 6.573 17124 Z= 0.278 Chirality : 0.033 0.134 1914 Planarity : 0.004 0.048 2182 Dihedral : 3.734 16.061 1675 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1505 helix: 1.93 (0.16), residues: 1063 sheet: -1.55 (1.38), residues: 10 loop : -1.50 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 675 TYR 0.014 0.001 TYR F 663 PHE 0.015 0.001 PHE F 432 TRP 0.012 0.001 TRP F 638 HIS 0.005 0.001 HIS G 580 Details of bonding type rmsd covalent geometry : bond 0.00268 (12689) covalent geometry : angle 0.49979 (17124) hydrogen bonds : bond 0.03788 ( 841) hydrogen bonds : angle 4.27360 ( 2472) *********************** 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 163 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.643 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: 0.8467 (mt-10) cc_final: 0.8261 (mt-10) REVERT: F 481 ASP cc_start: 0.9410 (m-30) cc_final: 0.9049 (p0) REVERT: F 723 TYR cc_start: 0.7995 (t80) cc_final: 0.7157 (t80) REVERT: F 797 ARG cc_start: 0.9076 (tpt-90) cc_final: 0.8752 (tpp-160) REVERT: F 804 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8976 (tm-30) REVERT: G 39 TYR cc_start: 0.8113 (p90) cc_final: 0.7546 (p90) REVERT: G 715 SER cc_start: 0.9480 (m) cc_final: 0.9067 (p) REVERT: G 769 MET cc_start: 0.8074 (tmm) cc_final: 0.7871 (tmm) REVERT: u 65 ASN cc_start: 0.9395 (p0) cc_final: 0.8851 (p0) REVERT: v 60 MET cc_start: 0.8258 (ptt) cc_final: 0.7891 (tmm) REVERT: v 78 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8749 (mmmt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2422 time to fit residues: 58.0561 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 : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054986 restraints weight = 217170.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.057187 restraints weight = 108531.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.058702 restraints weight = 67236.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.059689 restraints weight = 47580.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060350 restraints weight = 37339.365| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3039 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= 0.142 Angle : 0.512 7.111 17124 Z= 0.285 Chirality : 0.034 0.155 1914 Planarity : 0.004 0.048 2182 Dihedral : 3.754 17.291 1675 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.22), residues: 1505 helix: 1.93 (0.16), residues: 1064 sheet: -1.65 (1.37), residues: 10 loop : -1.51 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 318 TYR 0.023 0.001 TYR G 427 PHE 0.029 0.001 PHE G 828 TRP 0.010 0.001 TRP F 638 HIS 0.007 0.001 HIS G 378 Details of bonding type rmsd covalent geometry : bond 0.00300 (12689) covalent geometry : angle 0.51177 (17124) hydrogen bonds : bond 0.03834 ( 841) hydrogen bonds : angle 4.31743 ( 2472) *********************** 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 163 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.679 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: F 292 ASP cc_start: 0.8004 (m-30) cc_final: 0.7797 (m-30) REVERT: F 299 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8279 (mt-10) REVERT: F 481 ASP cc_start: 0.9432 (m-30) cc_final: 0.9055 (p0) REVERT: F 565 MET cc_start: 0.8926 (tmm) cc_final: 0.8576 (tmm) REVERT: F 723 TYR cc_start: 0.8004 (t80) cc_final: 0.7175 (t80) REVERT: F 797 ARG cc_start: 0.9093 (tpt-90) cc_final: 0.8761 (tpp-160) REVERT: F 804 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8983 (tm-30) REVERT: G 39 TYR cc_start: 0.8121 (p90) cc_final: 0.7556 (p90) REVERT: G 258 GLU cc_start: 0.8943 (tt0) cc_final: 0.8356 (tp30) REVERT: G 715 SER cc_start: 0.9473 (m) cc_final: 0.9069 (p) REVERT: G 769 MET cc_start: 0.8145 (tmm) cc_final: 0.7945 (tmm) REVERT: v 60 MET cc_start: 0.8199 (ptt) cc_final: 0.7892 (tmm) REVERT: v 78 LYS cc_start: 0.9062 (mmpt) cc_final: 0.8668 (mmmt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2611 time to fit residues: 61.4198 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 : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.066935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054325 restraints weight = 217222.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056534 restraints weight = 109803.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.058018 restraints weight = 68052.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058984 restraints weight = 48324.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059621 restraints weight = 38001.209| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12689 Z= 0.174 Angle : 0.526 6.680 17124 Z= 0.296 Chirality : 0.034 0.170 1914 Planarity : 0.004 0.047 2182 Dihedral : 3.805 18.014 1675 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1505 helix: 1.79 (0.16), residues: 1074 sheet: -1.82 (1.28), residues: 10 loop : -1.65 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 764 TYR 0.023 0.001 TYR G 427 PHE 0.021 0.001 PHE F 839 TRP 0.010 0.001 TRP F 638 HIS 0.006 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00358 (12689) covalent geometry : angle 0.52620 (17124) hydrogen bonds : bond 0.03875 ( 841) hydrogen bonds : angle 4.39425 ( 2472) *********************** 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 161 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.692 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: 0.8511 (mt-10) cc_final: 0.8239 (mt-10) REVERT: F 481 ASP cc_start: 0.9379 (m-30) cc_final: 0.8984 (p0) REVERT: F 723 TYR cc_start: 0.8021 (t80) cc_final: 0.7218 (t80) REVERT: F 797 ARG cc_start: 0.9045 (tpt-90) cc_final: 0.8752 (tpp-160) REVERT: F 804 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8975 (tm-30) REVERT: G 39 TYR cc_start: 0.7967 (p90) cc_final: 0.7387 (p90) REVERT: G 258 GLU cc_start: 0.8965 (tt0) cc_final: 0.8272 (tp30) REVERT: G 408 MET cc_start: 0.8389 (mmp) cc_final: 0.8111 (mmp) REVERT: G 715 SER cc_start: 0.9480 (m) cc_final: 0.9074 (p) REVERT: u 65 ASN cc_start: 0.9444 (p0) cc_final: 0.8939 (p0) REVERT: v 60 MET cc_start: 0.8194 (ptt) cc_final: 0.7946 (tmm) REVERT: v 78 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8683 (mmmt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2644 time to fit residues: 61.6568 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 0.0000 chunk 100 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.067710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055064 restraints weight = 215414.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057300 restraints weight = 108230.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058830 restraints weight = 66785.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.059815 restraints weight = 47232.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060485 restraints weight = 37027.375| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3149 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= 0.113 Angle : 0.509 6.975 17124 Z= 0.278 Chirality : 0.034 0.155 1914 Planarity : 0.005 0.100 2182 Dihedral : 3.781 17.903 1675 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.22), residues: 1505 helix: 1.97 (0.16), residues: 1063 sheet: -1.81 (1.29), residues: 10 loop : -1.45 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 415 TYR 0.014 0.001 TYR F 678 PHE 0.019 0.001 PHE F 432 TRP 0.007 0.001 TRP F 638 HIS 0.005 0.001 HIS G 378 Details of bonding type rmsd covalent geometry : bond 0.00250 (12689) covalent geometry : angle 0.50949 (17124) hydrogen bonds : bond 0.03759 ( 841) hydrogen bonds : angle 4.20064 ( 2472) ********************** 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 162 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.662 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: 0.7984 (m-30) cc_final: 0.7776 (m-30) REVERT: F 299 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8192 (mt-10) REVERT: F 481 ASP cc_start: 0.9424 (m-30) cc_final: 0.9048 (p0) REVERT: F 723 TYR cc_start: 0.8033 (t80) cc_final: 0.7223 (t80) REVERT: F 797 ARG cc_start: 0.9049 (tpt-90) cc_final: 0.8745 (tpp-160) REVERT: F 804 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8976 (tm-30) REVERT: G 39 TYR cc_start: 0.7998 (p90) cc_final: 0.7661 (p90) REVERT: G 258 GLU cc_start: 0.8928 (tt0) cc_final: 0.8335 (tp30) REVERT: G 715 SER cc_start: 0.9470 (m) cc_final: 0.9066 (p) REVERT: v 60 MET cc_start: 0.8217 (ptt) cc_final: 0.7886 (tmm) REVERT: v 78 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8553 (mmmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2409 time to fit residues: 56.5736 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 : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.067646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055023 restraints weight = 214874.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057261 restraints weight = 108334.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058778 restraints weight = 66820.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.059746 restraints weight = 47304.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060415 restraints weight = 37207.072| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12689 Z= 0.116 Angle : 0.498 6.171 17124 Z= 0.273 Chirality : 0.033 0.147 1914 Planarity : 0.004 0.077 2182 Dihedral : 3.709 19.220 1675 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.22), residues: 1505 helix: 2.00 (0.16), residues: 1065 sheet: -1.71 (1.35), residues: 10 loop : -1.46 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 871 TYR 0.011 0.001 TYR F 678 PHE 0.017 0.001 PHE F 432 TRP 0.007 0.001 TRP G 180 HIS 0.005 0.001 HIS G 378 Details of bonding type rmsd covalent geometry : bond 0.00250 (12689) covalent geometry : angle 0.49848 (17124) hydrogen bonds : bond 0.03642 ( 841) hydrogen bonds : angle 4.14484 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.95 seconds wall clock time: 69 minutes 6.06 seconds (4146.06 seconds total)