Starting phenix.real_space_refine on Thu Jul 2 05:40:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw5_54299/07_2026/9rw5_54299.cif" } resolution = 4.1 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: 4 Type Number sf(0) Gaussians P 84 5.49 5 C 3808 2.51 5 N 1320 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "D" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 2247 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1475 Unresolved non-hydrogen angles: 1865 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 19, 'ARG:plan': 23, 'ASN:plan1': 18, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 800 Chain: "C" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 2247 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1475 Unresolved non-hydrogen angles: 1865 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 19, 'ARG:plan': 23, 'ASN:plan1': 18, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 800 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain breaks: 1 Time building chain proxies: 1.87, per 1000 atoms: 0.27 Number of scatterers: 6832 At special positions: 0 Unit cell: (84.8, 109.18, 168.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 84 15.00 O 1620 8.00 N 1320 7.00 C 3808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 511.9 milliseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 71.8% alpha, 5.7% beta 35 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 4.026A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 removed outlier: 3.805A pdb=" N ARG B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 25 removed outlier: 4.002A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.517A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.837A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 617 through 630 removed outlier: 4.806A pdb=" N ASP D 621 " --> pdb=" O ASP D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 676 through 688 removed outlier: 3.987A pdb=" N GLN D 680 " --> pdb=" O PRO D 676 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 683 " --> pdb=" O ASP D 679 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 684 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 Processing helix chain 'D' and resid 698 through 714 Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 726 through 744 removed outlier: 4.598A pdb=" N GLN D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 773 Processing helix chain 'D' and resid 780 through 787 Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 802 removed outlier: 4.382A pdb=" N GLY D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 816 Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.612A pdb=" N GLU C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.621A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 535 through 554 Processing helix chain 'C' and resid 594 through 600 removed outlier: 4.007A pdb=" N THR C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.549A pdb=" N VAL C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 630 Processing helix chain 'C' and resid 639 through 652 Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 662 through 670 Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.107A pdb=" N GLN C 680 " --> pdb=" O PRO C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 693 Processing helix chain 'C' and resid 698 through 714 Processing helix chain 'C' and resid 714 through 723 Processing helix chain 'C' and resid 726 through 744 removed outlier: 4.519A pdb=" N GLN C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 773 removed outlier: 3.666A pdb=" N VAL C 750 " --> pdb=" O LYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 788 removed outlier: 4.230A pdb=" N ARG C 788 " --> pdb=" O ILE C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 801 Processing helix chain 'C' and resid 803 through 816 Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 531 through 533 removed outlier: 5.473A pdb=" N ILE D 573 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 565 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 556 through 559 removed outlier: 6.620A pdb=" N ILE D 556 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 614 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 558 " --> pdb=" O VAL D 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'C' and resid 531 through 533 removed outlier: 5.628A pdb=" N ILE C 573 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 565 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 556 through 559 removed outlier: 6.744A pdb=" N ILE C 556 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 614 " --> pdb=" O ILE C 556 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 558 " --> pdb=" O VAL C 614 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1108 1.29 - 1.37: 1407 1.37 - 1.45: 844 1.45 - 1.53: 3330 1.53 - 1.61: 341 Bond restraints: 7030 Sorted by residual: bond pdb=" N1 C F 18 " pdb=" C6 C F 18 " ideal model delta sigma weight residual 1.367 1.386 -0.019 6.00e-03 2.78e+04 9.65e+00 bond pdb=" N1 C F 19 " pdb=" C6 C F 19 " ideal model delta sigma weight residual 1.367 1.385 -0.018 6.00e-03 2.78e+04 9.19e+00 bond pdb=" N1 C F 29 " pdb=" C6 C F 29 " ideal model delta sigma weight residual 1.367 1.385 -0.018 6.00e-03 2.78e+04 8.64e+00 bond pdb=" N1 C F 38 " pdb=" C6 C F 38 " ideal model delta sigma weight residual 1.367 1.383 -0.016 6.00e-03 2.78e+04 6.90e+00 bond pdb=" N1 C F 27 " pdb=" C6 C F 27 " ideal model delta sigma weight residual 1.367 1.382 -0.015 6.00e-03 2.78e+04 6.15e+00 ... (remaining 7025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 9184 1.05 - 2.10: 757 2.10 - 3.15: 144 3.15 - 4.20: 18 4.20 - 5.25: 5 Bond angle restraints: 10108 Sorted by residual: angle pdb=" N6 A F 8 " pdb=" C6 A F 8 " pdb=" N1 A F 8 " ideal model delta sigma weight residual 118.60 114.72 3.88 6.00e-01 2.78e+00 4.19e+01 angle pdb=" N6 A F 30 " pdb=" C6 A F 30 " pdb=" N1 A F 30 " ideal model delta sigma weight residual 118.60 115.44 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" N6 A F 44 " pdb=" C6 A F 44 " pdb=" N1 A F 44 " ideal model delta sigma weight residual 118.60 115.47 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" C6 A F 13 " pdb=" C5 A F 13 " pdb=" C4 A F 13 " ideal model delta sigma weight residual 117.00 114.47 2.53 5.00e-01 4.00e+00 2.55e+01 angle pdb=" N6 A F 10 " pdb=" C6 A F 10 " pdb=" N1 A F 10 " ideal model delta sigma weight residual 118.60 115.68 2.92 6.00e-01 2.78e+00 2.37e+01 ... (remaining 10103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 3985 23.62 - 47.25: 142 47.25 - 70.87: 107 70.87 - 94.50: 20 94.50 - 118.12: 6 Dihedral angle restraints: 4260 sinusoidal: 1318 harmonic: 2942 Sorted by residual: dihedral pdb=" C5' U F 39 " pdb=" C4' U F 39 " pdb=" C3' U F 39 " pdb=" O3' U F 39 " ideal model delta sinusoidal sigma weight residual 82.00 107.82 -25.82 1 8.00e+00 1.56e-02 1.50e+01 dihedral pdb=" C3' U F 39 " pdb=" C4' U F 39 " pdb=" O4' U F 39 " pdb=" C1' U F 39 " ideal model delta sinusoidal sigma weight residual 20.00 -5.81 25.81 1 8.00e+00 1.56e-02 1.50e+01 dihedral pdb=" O4' U F 39 " pdb=" C4' U F 39 " pdb=" C3' U F 39 " pdb=" C2' U F 39 " ideal model delta sinusoidal sigma weight residual -35.00 -9.33 -25.67 1 8.00e+00 1.56e-02 1.48e+01 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 892 0.030 - 0.061: 321 0.061 - 0.091: 95 0.091 - 0.121: 76 0.121 - 0.152: 12 Chirality restraints: 1396 Sorted by residual: chirality pdb=" C2' U F 39 " pdb=" C3' U F 39 " pdb=" O2' U F 39 " pdb=" C1' U F 39 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" C4' U F 35 " pdb=" C5' U F 35 " pdb=" O4' U F 35 " pdb=" C3' U F 35 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" C1' A E 13 " pdb=" O4' A E 13 " pdb=" C2' A E 13 " pdb=" N9 A E 13 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1393 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G F 34 " -0.057 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" N9 G F 34 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G F 34 " 0.021 2.00e-02 2.50e+03 pdb=" N7 G F 34 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G F 34 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G F 34 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G F 34 " -0.025 2.00e-02 2.50e+03 pdb=" N1 G F 34 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G F 34 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G F 34 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G F 34 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G F 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 16 " 0.040 2.00e-02 2.50e+03 2.36e-02 1.25e+01 pdb=" N1 C F 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C F 16 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C F 16 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C F 16 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C F 16 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C F 16 " 0.041 2.00e-02 2.50e+03 pdb=" C5 C F 16 " -0.022 2.00e-02 2.50e+03 pdb=" C6 C F 16 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 39 " -0.044 2.00e-02 2.50e+03 2.28e-02 1.16e+01 pdb=" N1 U F 39 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U F 39 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U F 39 " 0.028 2.00e-02 2.50e+03 pdb=" N3 U F 39 " -0.016 2.00e-02 2.50e+03 pdb=" C4 U F 39 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U F 39 " -0.021 2.00e-02 2.50e+03 pdb=" C5 U F 39 " 0.021 2.00e-02 2.50e+03 pdb=" C6 U F 39 " 0.024 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2220 2.82 - 3.34: 7091 3.34 - 3.86: 11965 3.86 - 4.38: 11608 4.38 - 4.90: 17537 Nonbonded interactions: 50421 Sorted by model distance: nonbonded pdb=" O PRO C 118 " pdb=" N ARG C 120 " model vdw 2.298 3.120 nonbonded pdb=" O2' U E 35 " pdb=" O5' U E 36 " model vdw 2.335 3.040 nonbonded pdb=" O PRO D 118 " pdb=" N ARG D 120 " model vdw 2.365 3.120 nonbonded pdb=" O ILE D 67 " pdb=" N ASN D 78 " model vdw 2.408 3.120 nonbonded pdb=" O2' U E 36 " pdb=" O5' G E 37 " model vdw 2.431 3.040 ... (remaining 50416 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.003 0.033 7030 Z= 0.305 Angle : 0.647 5.251 10108 Z= 0.646 Chirality : 0.041 0.152 1396 Planarity : 0.003 0.024 1092 Dihedral : 18.204 118.121 2324 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.68 (0.26), residues: 998 helix: 1.24 (0.20), residues: 656 sheet: -2.23 (0.61), residues: 52 loop : -0.73 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.31 ( 7030) covalent geometry : angle 0.64670 / 0.65 (10108) hydrogen bonds : bond 0.12490 / 9.55 ( 608) hydrogen bonds : angle 6.02222 / 4.81 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0246 time to fit residues: 1.6796 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.086801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071627 restraints weight = 45422.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070854 restraints weight = 56218.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069611 restraints weight = 55769.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069211 restraints weight = 58162.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 91)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068768 restraints weight = 56062.924| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7030 Z= 0.364 Angle : 0.709 9.575 10108 Z= 0.452 Chirality : 0.046 0.193 1396 Planarity : 0.005 0.024 1092 Dihedral : 18.549 113.306 2324 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.08 (0.25), residues: 998 helix: 0.72 (0.19), residues: 662 sheet: -2.19 (0.64), residues: 52 loop : -0.88 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.36 ( 7030) covalent geometry : angle 0.70916 / 0.45 (10108) hydrogen bonds : bond 0.08002 / 6.04 ( 608) hydrogen bonds : angle 5.80474 / 4.63 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0309 time to fit residues: 2.1365 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.087460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.072438 restraints weight = 44997.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071547 restraints weight = 66330.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.071332 restraints weight = 58260.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070578 restraints weight = 57688.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.070691 restraints weight = 55101.159| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7030 Z= 0.218 Angle : 0.461 5.944 10108 Z= 0.300 Chirality : 0.039 0.184 1396 Planarity : 0.003 0.012 1092 Dihedral : 18.396 113.115 2324 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.39 (0.26), residues: 998 helix: 1.84 (0.20), residues: 662 sheet: -2.33 (0.62), residues: 52 loop : -0.57 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.22 ( 7030) covalent geometry : angle 0.46051 / 0.30 (10108) hydrogen bonds : bond 0.05540 / 4.15 ( 608) hydrogen bonds : angle 4.94870 / 3.95 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.142 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0241 time to fit residues: 1.6576 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 60.0000 chunk 25 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.085477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069758 restraints weight = 45182.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069080 restraints weight = 59112.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068404 restraints weight = 59477.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068111 restraints weight = 57569.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067879 restraints weight = 55280.055| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7030 Z= 0.330 Angle : 0.661 7.466 10108 Z= 0.420 Chirality : 0.046 0.225 1396 Planarity : 0.004 0.022 1092 Dihedral : 18.653 118.622 2324 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.14 (0.26), residues: 998 helix: 0.84 (0.19), residues: 662 sheet: -2.90 (0.64), residues: 36 loop : -1.08 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.33 ( 7030) covalent geometry : angle 0.66126 / 0.42 (10108) hydrogen bonds : bond 0.07184 / 5.43 ( 608) hydrogen bonds : angle 5.73361 / 4.57 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0298 time to fit residues: 2.0835 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.085947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070053 restraints weight = 45123.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069209 restraints weight = 57091.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 83)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068518 restraints weight = 51473.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068059 restraints weight = 51767.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 80)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.067694 restraints weight = 53077.484| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7030 Z= 0.253 Angle : 0.498 5.482 10108 Z= 0.322 Chirality : 0.040 0.201 1396 Planarity : 0.003 0.015 1092 Dihedral : 18.541 116.791 2324 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.82 (0.27), residues: 998 helix: 1.44 (0.20), residues: 662 sheet: -3.07 (0.61), residues: 36 loop : -0.94 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.25 ( 7030) covalent geometry : angle 0.49779 / 0.32 (10108) hydrogen bonds : bond 0.05733 / 4.31 ( 608) hydrogen bonds : angle 5.13183 / 4.07 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0292 time to fit residues: 1.9848 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 40.0000 chunk 103 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 0.1980 chunk 74 optimal weight: 50.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.085323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069974 restraints weight = 45385.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069116 restraints weight = 60949.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068344 restraints weight = 58260.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067725 restraints weight = 62170.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067859 restraints weight = 53542.836| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7030 Z= 0.264 Angle : 0.537 6.403 10108 Z= 0.346 Chirality : 0.041 0.226 1396 Planarity : 0.003 0.015 1092 Dihedral : 18.545 117.750 2324 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.72 (0.27), residues: 998 helix: 1.42 (0.20), residues: 662 sheet: -3.62 (0.57), residues: 36 loop : -1.06 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.26 ( 7030) covalent geometry : angle 0.53745 / 0.35 (10108) hydrogen bonds : bond 0.06161 / 4.64 ( 608) hydrogen bonds : angle 5.25239 / 4.17 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0277 time to fit residues: 1.8721 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 54 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.072053 restraints weight = 44626.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070961 restraints weight = 64988.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.071203 restraints weight = 61616.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070626 restraints weight = 55697.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.070791 restraints weight = 52351.985| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 7030 Z= 0.132 Angle : 0.383 4.602 10108 Z= 0.248 Chirality : 0.036 0.199 1396 Planarity : 0.002 0.011 1092 Dihedral : 18.439 114.388 2324 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.88 (0.28), residues: 998 helix: 2.38 (0.20), residues: 662 sheet: -3.73 (0.54), residues: 36 loop : -0.72 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.13 ( 7030) covalent geometry : angle 0.38340 / 0.25 (10108) hydrogen bonds : bond 0.04651 / 3.48 ( 608) hydrogen bonds : angle 4.49151 / 3.55 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0288 time to fit residues: 1.9400 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.0010 chunk 54 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 47 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.087105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071736 restraints weight = 45147.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070806 restraints weight = 57138.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070432 restraints weight = 53139.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070353 restraints weight = 45235.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.070057 restraints weight = 45706.713| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7030 Z= 0.145 Angle : 0.384 4.754 10108 Z= 0.248 Chirality : 0.036 0.201 1396 Planarity : 0.002 0.012 1092 Dihedral : 18.284 113.173 2324 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 2.14 (0.28), residues: 998 helix: 2.58 (0.20), residues: 662 sheet: -3.69 (0.55), residues: 36 loop : -0.62 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.14 ( 7030) covalent geometry : angle 0.38397 / 0.25 (10108) hydrogen bonds : bond 0.04710 / 3.53 ( 608) hydrogen bonds : angle 4.36502 / 3.45 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0287 time to fit residues: 1.9273 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.086259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.070404 restraints weight = 44807.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069847 restraints weight = 58390.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069248 restraints weight = 45627.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068636 restraints weight = 53078.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068959 restraints weight = 43961.380| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7030 Z= 0.199 Angle : 0.443 5.579 10108 Z= 0.286 Chirality : 0.038 0.213 1396 Planarity : 0.003 0.014 1092 Dihedral : 18.286 115.812 2324 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.62 (0.27), residues: 998 helix: 2.15 (0.20), residues: 662 sheet: -3.76 (0.58), residues: 36 loop : -0.75 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.20 ( 7030) covalent geometry : angle 0.44290 / 0.29 (10108) hydrogen bonds : bond 0.05298 / 3.99 ( 608) hydrogen bonds : angle 4.64352 / 3.68 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0238 time to fit residues: 1.6243 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 20.0000 chunk 46 optimal weight: 0.1980 chunk 102 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 18 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 overall best weight: 5.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.085317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.070455 restraints weight = 44660.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069818 restraints weight = 58504.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069044 restraints weight = 53434.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068389 restraints weight = 55039.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068238 restraints weight = 56717.606| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7030 Z= 0.243 Angle : 0.505 6.284 10108 Z= 0.327 Chirality : 0.040 0.237 1396 Planarity : 0.003 0.014 1092 Dihedral : 18.392 117.290 2324 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.02 (0.27), residues: 998 helix: 1.67 (0.20), residues: 662 sheet: -4.18 (0.77), residues: 24 loop : -1.06 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.24 ( 7030) covalent geometry : angle 0.50515 / 0.33 (10108) hydrogen bonds : bond 0.05893 / 4.44 ( 608) hydrogen bonds : angle 5.05373 / 4.01 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0241 time to fit residues: 1.6990 Evaluate side-chains 32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 28 optimal weight: 70.0000 chunk 86 optimal weight: 0.1980 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 overall best weight: 7.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.084400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069317 restraints weight = 44213.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068551 restraints weight = 63027.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068220 restraints weight = 55742.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067789 restraints weight = 59673.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067889 restraints weight = 49875.336| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7030 Z= 0.319 Angle : 0.586 6.680 10108 Z= 0.380 Chirality : 0.043 0.254 1396 Planarity : 0.004 0.021 1092 Dihedral : 18.589 118.229 2324 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 0.25 (0.27), residues: 998 helix: 1.04 (0.20), residues: 672 sheet: -4.30 (0.77), residues: 24 loop : -1.38 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE D 16 TRP 0.000 0.000 TRP D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.32 ( 7030) covalent geometry : angle 0.58629 / 0.38 (10108) hydrogen bonds : bond 0.06651 / 5.02 ( 608) hydrogen bonds : angle 5.49736 / 4.36 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.98 seconds wall clock time: 20 minutes 3.96 seconds (1203.96 seconds total)